HE IS HOW PURDUE MAIL LIST FILTERS THE MAIL

Re: EMAIL ABUSE - how to stop
From: Adam Treister (a...@treestar.com)
Date: Mon Dec 16 2002 - 16:00:07 EST

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On Thursday, December 12, 2002, at 05:43 AM, J.Paul Robinson wrote:

Paul,

Sounds like you're advocating fighting disease by eradicating the
antigen instead of boosting the immune response.  You can organize
all
you want on eliminating the pest, but until they put a stamp tax on
email, a better approach is to let the
messages be out there, but have them filtered to oblivion before you
ever see them.

In your case, the postmaster at Purdue is probably already filtering
millions of messages a day that come to the thousands of email users
on
campus. They are probably capable of shutting down any RNWAY mail,
and
spreading the word to other postmasters that they also should filter
those messages.

So if you can get the IT people at the university to tighten their
sieve, that's best. Otherwise you have to switch to an email program
that has good junk filters.  I think I get 500+ messages a day, and
only 10 to 20 make it past the junk filter.
Until last summer I was using Outlook Express and spam was a huge
problem. Since then I switched to the free Mail program in OS X,
which
just added special features for spam detection and removal.  Its
probably 97% effective, and I haven't found any false positives.
So, of course, the best answer is to get a Mac  :)

I'm sure the PC mail clients are addressing this issue as well.  I
believe there are central databases of offenders so programs can
learn
from others which messages to delete.   I would imagine this is the
most important feature in any email program sold these days, so I bet
Eudora or other third party mail programs have this solved.

There's a lot of information on the subject at:

http://spam.abuse.net/

Whether you fight the problem on the server or the client, it
definitely is worth getting it cleaned up.   I found it screwed up my
whole communications process because every time I wanted check email,
I
had to wade through dozens or hundreds of useless ads.

Adam

---------------------------------------------------
Adam Treister
a...@treestar.com
www.flowjo.com  800-366-6045
---------------------------------------------------

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COMMERCIAL CHAT FOR SPECIAL VENDORS....YOU WILL NOT SEE THESE POST
ANYWHERE ELSE!

THE PROOF IS BEING DYSTROYED AS THE ARCHIVES ARE REMOVED!

From: J. Paul Robinson <j...@flowcyt.cyto.purdue.edu>
Date: Fri Dec 28 2007 - 13:43:46 EST
Beware, the end is nigh!

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!

PUCL- DELETES OR DIABLES  LINKS THAT ARE EVIDENCE OF EXCLUSIVE
VENDORS
AND PROOF OF FILTERING OUT VENDORS!

From : J. Paul Robinson <j...@flowcyt.cyto.purdue.edu> ... I will
probably get into seriuous trouble for what I am about to say, but
what the heck, ...

www.cyto.purdue.edu/hmarchiv/2005/0587.htm - 14k - Cached - Similar
pages - Note this
[ More results from www.cyto.purdue.edu ]

http://index.cc.purdue.edu:8765/query.html?col=pumerge&qt=purdue+cyto...

ALL INFORMATION MUST BE TAKEN FROM VERITYHOUSE SOFTWARE SERVER

SAC Homepage - How do I join the Purdue Cytometry Discussion Group? -
8 visits - 2:01pm
Answer: The Purdue Cytometry discussion group is strictly for
discussion of scientific issues relating to the fields in which ISAC
is generally involved. ...
www.isac-net.org/content/view/16/78/ - 14k - Cached - Similar pages -
Note this

Re: [Fwd: flow cytometry
software will you trust Purdue..Lets play MONOPOLY]

***************************************************************************­-
********************************************************

Larry, we have about 3000 people on the Purdue discussion list which
is

primarily about cytometry - and a lot of flow cytometry - to join,

people actually have to go through me, and we review every person who

comes on.

***************************************************************************­-
********************************************************

Larry, we have about 3000 people on the Purdue discussion list which
is

primarily about cytometry - and a lot of flow cytometry - to join,

people actually have to go through me, and we review every person who

comes on.

Standard
Header|Full
Message View

J. Paul Robinson
<j...@flowcyt.cyto.purdue.edu>

ViewMonday, November 19, 2007 2:14:38 PM

To:Larry Farrell <farrl...@isu.edu>; mitchell haynes
<buybro...@yahoo.com>;
skel...@flowcyt.cyto.purdue.edu; Bartek Rajwa
ra...@flowcyt.cyto.purdue.edu

****Larry, we have about 3000 people on the Purdue discussion list
which is

primarily about cytometry - and a lot of flow cytometry - to join,

people actually have to go through me, and we review every person who

comes on.
***************************************************************************­-
******************************************************

Larry

Sorry you are experiencing a problem

From the header - This is apparently coming from a Mitchel Haynes

mitchell haynes <buybro...@yahoo.com>
- is this correct?

I initially thought messages coming from this person were a scam and

challenged them when they started posting to our list as well. I had

someone do a check on them. it is apparent that they have written
some

software and they think its ants-pants. They have tried to post
things

on the Purdue list, they have used every possible website and email

discussion group to get cross listed to boost their ratings on
Google.

Basically I view their behavior as very tenuous and from the message
you

sent me, it appears that it is not appropriate to do what they are
doing...

I have taken the following action:

1. Steve Kelley has been instructed to remove their email and any

postings on the Purdue list. They are now banned

2. I am going to Copying Bartek Rajwa the editor of the ISAC site to

beware of them

3. I am contacting Google and other sites to let
them know that these

people are self-propagating links.

4. If I see any message that in any way impunes Purdue or our

reputation, I will go after them with every possible legal recourse
at

my disposal. We will not allow our reputation to suffer because of

commercial abuse.

5. You should ban this address, and basically indicate to your
members

that this is a scam. While they claim to be legitimate, they are
acting

exactly as any scam artist...I already told them that they were
acting

as scammers and they got upset with me...well, if they don't desist,

they will find out how much influence we actually have...

I will check the message

MONOPOLY

and see if this is actually libelous - it appears to be - and if it
is,

I will close this person down really, really fast!!! (Steve please
check

out this message and make a copy)

Larry, we have about 3000 people on the Purdue discussion list which
is

primarily about cytometry - and a lot of flow cytometry - to join,

people actually have to go through me, and we review every person who

comes on.

I am sorry you are experiencing this problem, and we are happy to
help

in any way we can.

regards

paul Robinson

Professor, Purdue

*****************************************Larry, we have about 3000
people on the Purdue discussion list which is

primarily about cytometry - and a lot of flow cytometry - to join,

people actually have to go through me, and we review every person who

comes on.
***************************************************************************­-
************

WITH EVERY INTERNATIONAL OUTLET THE MAIL LIST HAS WHY????WHY????WHY

3,000 PEOPLE ON THE LIST...

DOES IT SAY......THEY MUST HAVE TO GOT THROUGH WHO?

ONLY 3,000 PEOPLE?

IT IS INTERNATIONAL~!

***************************************************************************­-
***********************************************
2007 End of year message from Purdue
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From: J. Paul Robinson <j...@flowcyt.cyto.purdue.edu>
Date: Fri Dec 28 2007 - 13:43:46 EST
Beware, the end is nigh!
No, not an apocalyptic prediction - but 2007 is definitely coming to
an
end. Not before time I would say - it s been a busy year. But I have
some strong words to end the year and I am going to say them!! Of
course
you don t have to read them!

Cytometry is now 40 years old and it s been sort of decaying a bit.
What
do I mean? I am amazed at how conservative and frankly boring the
field
has become. Why? It s time to move to the 21st century folks. I'm
getting older and frankly, its time to kick some butt as my younger
colleagues often say. We talk so much like it is the same old
cytometry
it has always been. Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!
True we need to do the core work and do it well, but lets not forget
that fundamental tools of cell analysis are changing and if we don't
keep ourselves up-to-date and educated on what's happening....before
we
know it, a new field will emerge and we will be like the old electron
microscopists who are still wondering what happened ......

I know most of us work in the field and like what we do, but I think
its
time to open up a little and try to do some serious integration of
our
field. It s not happening very effectively on the most part I would
say.
Cytometry is about integration of the tools of the field into the
vast
reaches of biological problems that we can contribute to solving.
Cytometry is about advancement of the field, that means always
looking
ahead. ISAC will soon be the International Society for Advancement of
Cytometry   a 21st century Society not a 20th century Society.

Cytometry is not flow cytometry!! Let s not kid ourselves about this
folks. Cytometry is about measuring cells - however you do it - and
flow
cytometry is just one component of many. I understand that it may be
the
only tool some of you use - I don t want to take away from that or
de-emphasize its value or importance. But, we so often hear people
talk
about our field only in context of just flow cytometry. Recently,
when
we polled the ISAC community on changing our name from "analytical
Cytology" to Advancement of Cytometry" we received comments like "hey
I
don t do flow cytometry, so why are you reducing the breadth of the
field?" Ouch - they think "cytometry" means "flow cytometry". We have
a
long way to go before we convince the community that we cover all
aspects of cytometry. And let s also remember the growing membership
in
India and China   (that s half the worlds population right there)
it
s
high time we paid much more attention to these countries as a field.
Awtar Krishan can t be the only person to drive cytometry training
and
education for 1.2 billion Indians can he? Well he has been up to now.
Who is taking on the mantle of training and education of cytometry in
China?

So here's the scoop. That's one of the reasons why the Purdue Web
portal
is going to change. We tried to make the change this past year, but
there were too many other things happening here to achieve it. But
come
middle of 2008, I am resolved that you will see a huge difference in
the
Purdue site. It s been the default cytometry communication portal now
for many, many years. We have focused on good clean fun with
cytometry
-
quality, timely, simple - no spam. Many people like that actually.
The
portal is almost overwhelming for us   22,000 daily page requests
with
over 2 Gigs daily download. In 2007 alone, downloads of 208,000
powerpoint files, 233,000 PDF files, 8800 movies, 38,000 word
document
files. The education pages and the Cytometry Discussion Archive are
the
most hit for sure. Over 125,000 distinct files from our portal were
accessed in 2007.

But all good things must come to an end. Come July 2008, the usual
Purdue web portal may well be no more. It will be replaced with
something entirely new. Hopefully most will find it more useful and
relevant - some will not like it. Maybe we will be able to make
everyone
happy....ha!..C'est la vie. Some of you will be beta testers and
advisers I hope.

So my best wishes to all in the cytometry field for 2008. Regarding
the
past year on the discussion list, its been lively, with an average of
7
messages per day with 754 different individuals submitting at least
one
message. 139 messages had at least 6 responses.  There were 1205
unique
subject lines. Subscribers came from 64 top level domains. The usual
bunch of suspects answered lots of messages and Marty Bigos seems to
have too much time as he answered the most (thanks Marty!!).
Tragically,
the second most prolific responder was Randy Fisher who passed away
on
December 5.  Randy's responses were always short, to the point and
accurate. It hurts to lose one of our own, particularly when it's one
of
our most active members. But that s the point isn't it. For many
years
to come, we have the value of Randy's hundreds of suggestions over
the
years archived for the many new people who enter our field. Many of
you
probably never actually met Randy - but I bet most of you feel you
knew
him. One of the mysteries of the web I suppose. Our condolences to
Randy's family - perhaps they didn't know how many people knew Randy
"electronically" - but we all did. You know we are a small field when
it
comes to the big world of science so when we lose one person, the
entire
field morns.

To end 2007, let me make a big plug for a program we began at the
2006
ISAC congress. Gary Durack from iCyt and myself started a small
not-for-profit charity called "Cytometry for Life" in response to
Stephen Lewis' compelling plea for some low cost CD4 devices. Our
field
has done a lot of talking about this, but only a few people have
really
tried to do anything practical. Well, folks we have all been doing
cytometry for a very long time - it's time to do something.
"Cytometry
for life" (http://www.cytometryforlife.org) is working hard. We have
made tremendous progress in just one year. It would be great if you
all
decided to jump on board and play a small part. You can give money,
advice, moral support, talk to your politicians, community health-
care,
charities, whatever. But get involved as be recognized as the
cytometry
community to solve this problem of bringing low cost, portable
devices
to the 65% or more of African's who don t live in the cities and
towns
where current CD4 technologies are available. Our goal is to work in
areas not being served by current technologies. We have heard these
calls before, but folks we have to deal with this problem - it's your
problem if you call yourself a "cytometry" person. Email me if you
can
help - consider donating to the program, let's make it work. By the
end
of 2008, I want to be telling you that the program is getting to
people
who need this desperately. Help us achieve that for 2008.

I hope many of you got hold of a copy of our new double DVD set
Cytometry   60 years of Innovation    if not ask your local rep from
virtually any company in our field. It might give you a good sense of
how strong the foundation in our field really is. I will see many of
you
at the 2008 congress in Budapest. I know some of you think its going
to
be expensive so I took several hours myself and created a webpage for
the cheap ones out there so you have no excuses not to go...
(http://www.cyto.purdue.edu/flowcyt/cheapflights1.htm).

It's been a privilege to serve for the past 19 months as President of
ISAC. I will gladly pass that hat to Bob Murphy in May. ISAC is alive
and well  - membership is growing daily. I would not be surprised to
see
us top 2000 by the end of the Congress in May. I know that about 60%
of
the members of this list are NOT ISAC members. Perhaps you should
consider joining the Society that keeps many of you in business?
http://www.isac-net.org/

My best wishes for you all in 2008 from Purdue
Paul

--
J. Paul Robinson
SVM Professor of Cytomics
Professor of Immunopharmacology & Biomedical Engineering
Director, Purdue University Cytometry Laboratories
President, International Society for Analytical Cytology

***************************************************************************­-
**************************************************
From: J. Paul Robinson <j...@flowcyt.cyto.purdue.edu>
Date: Fri Dec 28 2007 - 13:43:46 EST
Beware, the end is nigh!
No, not an apocalyptic prediction - but 2007 is definitely coming to
an
end. Not before time I would say - it s been a busy year. But I have
some strong words to end the year and I am going to say them!! Of
course
you don t have to read them!

Cytometry is now 40 years old and it s been sort of decaying a bit.

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!
***************************************************************************­-

Verity House software
RE: gate-specific data cropping
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From: VSH Tech Support <T...@vsh.com>
Date: Fri Feb 16 2007 - 09:01:56 EST
Stevan

At the risk of sounding like a commercial, WinList can do exactly
what
you
want.  The problem of "sucking up air" or perhaps having a clogged
nozzle at
the end of a run has gotten all of us at one time or another, and
then
the
data (most of which is probably fine) appears to be unusable.
WinList
addresses this issue with the FTIM parameter, which is basically a
"chronology" parameter defined over 1024 channels.  Each event is
assigned
an FTIM channel based on its order in the listmode file, channel zero
having
the first n/1024 events, and channel 1023 having the last n/1024
events.

Displaying a 2P dot plot of FTIM vs. side scatter, for example, will
clearly
show the aberrant events.  You may then gate on the "good" events, or
gate
out the "bad" events.  Either way, you can salvage an otherwise bad
run.

You can also save the gated listmode using WinList's Save Data Source
option, and it will contain only
the "good" events.  Another feature of the Save Data Source option is
the
ability to set the number of events to save in the listmode file,
which at
least partially addresses the desire to save a larger file into
smaller
segments that will each have the same number of events within given
regions,
as you are requesting.

Best regards,
Don
Donald J. Herbert
Technical Support Manager
Verity Software House

-----Original Message-----
From: Stevan Lauriault [mailto:ste...@lauriault.com]
Sent: Friday, February 09, 2007 6:24 PM
To: cyto-inbox
Subject: Re: gate-specific data cropping

Thanks for your very helpful comments.  I guess what I am trying to
get
at
is this: is
there any analysis software available that can reduce list mode data
in a
reverse order-specific matter (in reverse sequence)?  Correct me if
I'm
wrong, but I believe this function would also help in the event that
a
user
lets a sample run dry and sucks up air bubbles, or over collects
their
intended gating target (for example, in acquisition and storage, 5000
of
R1).

Thanks,

Stevan
---------- Original Message ----------------------------------
From: "Byron Ellis" <bcel...@stanford.edu>
Date:  Wed, 7 Feb 2007 16:21:28 -0800

error between sample tubes.

of R3.

region. If we
crop

events in R3.

sizes.  We could

fluorescent signal than Ry.

captures the latter.

biomarker, among the subsets.

the

(R1,

data.

collected.

software?

________________________________________________________________
Sent via the WebMail system at lauriault.com
Received on Fri Feb 16 16:38:00 2007
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RE: DNA analysis software
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From: VSH Tech Support <T...@vsh.com>
Date: Wed Feb 21 2007 - 11:29:45 EST
Hello Ibtissam,

ModFit LT, for PC or Mac, has advanced modeling capability for
research
applications in DNA cell cycle analysis.  You may use any of the
model
templates the program offers, or create your own models for non-
traditional
analysis, including non-mammalian DNA cell cycle studies. ModFit LT
can be
linked to our WinList program to provide a complete cell cycle
analysis on
any number of sub-populations with a single click of a button.

For an overview, visit  <http://www.vsh.com/products>
http://www.vsh.com/products .

Best regards,

Don

Donald J. Herbert
Technical Support Manager
Verity Software House

________________________________

From: Ibtissam Abdul-Jabbar [mailto:iajab...@cicr.uq.edu.au]
Sent: Wednesday, February 14, 2007 11:41 PM
To: cyto-inbox
Subject: DNA analysis software

Dear All, before buying software to analyse DNA on PC, I would like
to
get
your opinion. I already have ModFit for Macintosh.

What are you using and what do you recommend for research purposes.

Is MultiCycle Av the one of choice?

I appreciate your comments.

Ibtissam A Jabbar (PhD)

Manager of the FACS facilities

Diamantina Institute for Cancer, Immunology and Metabolic Medicine
(DI)

The University of Queensland

Level 4 R Wing

Princess Alexandra Hospital

Ipswich Rd Buranda QLD 4102

Australia

Ph: 07 3240 5945

Fax: 07 3240 5946

Mob: 0401154744
Received on Thu Feb 22 15:18:00 2007
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Re: gate-specific data cropping
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From: WEHICytometry <facs_c...@wehi.EDU.AU>
Date: Mon Feb 12 2007 - 18:25:38 EST
Stevan,

For what it's worth, we have a utility we call Hackit that can crop
cells from the front or back of a FCS file ( see http://
www.wehi.edu.au/cytometry/freesoftware/index.html).  We use it for
the tasks you suggest in cleaning up violated data.  I don't know
how
useful that would be for your current purpose because it can't do
gating; numbers clipped are total cell numbers.  I guess if you knew
the proportions of your gated cells you could eventually clip out
the
file segments you need.

Frank Battye.

On 10/02/2007, at 10:24 AM, Stevan Lauriault wrote:

    |    |  << The Cytometry Laboratory
     \__/ <<<< The Walter & Eliza Hall Institute
------!!<<<<<< 1G Royal Parade, Parkville
     /!!\ <<<< Victoria 3050, Australia
    o !! \  << ph: 61_3_9345 2540, fax: 61_3_9347 0852
Received on Tue Feb 13 15:18:00 2007
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Re: gate-specific data cropping
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From: Stevan Lauriault <ste...@lauriault.com>
Date: Fri Feb 09 2007 - 18:24:07 EST
Thanks for your very helpful comments.  I guess what I am trying to
get
at is this: is
there any analysis software available that can reduce list mode data
in a reverse
order-specific matter (in reverse sequence)?  Correct me if I'm
wrong,
but I believe this
function would also help in the event that a user lets a sample run
dry and sucks up air
bubbles, or over collects their intended gating target (for example,
in acquisition and
storage, 5000 of R1).

Thanks,

Stevan
---------- Original Message ----------------------------------
From: "Byron Ellis" <bcel...@stanford.edu>
Date:  Wed, 7 Feb 2007 16:21:28 -0800

crop

the

(R1,

________________________________________________________________
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Received on Mon Feb 12 12:18:00 2007
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RE: gate-specific data cropping
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From: Nebe-Von-Caron, G <g.nebe-von-ca...@unipath.com>
Date: Thu Feb 08 2007 - 09:36:37 EST
The number of events collected will not be the influential thing as
with
a minimum of 500 events you get already a damn good estimate of your
MFI. Just as an educational exercise you should do is to look at MFI
estimate of one population over events. It should indicate that your
estimate if the sample mean after 100 "samples" (each cell being a
sample on its own) is already pretty good. You might want to look at
the
distribution of mean fluorescence or more important of single event
residuals (distance from mean) over time to see if they show a trend
which would indicate an unstable measurement.

In the sample you propose you are more likely to see differences
based
on compensation variation between your 3 populations which again is
independent of the number of events looked at if more than 500 have
been
measured. It would indeed be interesting to see how much variation
you
get in mfi between independent tubes as you are more likely to
increase
variation by the sample processing than by the measurement.

One control for your experiment would be to test the MFI distribution
by
swapping fluorochromes to demonstrate that you are independent of
compensation and to show that the change in MFI is not dependent of
steric hindrance or FRET, depending of the experimental / instrument
details.

Regards

Gerhard

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From: Byron Ellis <bcel...@stanford.edu>
Date: Wed Feb 07 2007 - 19:21:28 EST
On 2/7/07, Stevan Lauriault <ste...@lauriault.com> wrote:

that are isolated on a bivariate dot plot (FL1 vs. FL4), doing so in
separate sample
tubes would introduce the extra probability of experimental error
between sample tubes.
Directly comparing the subsets from the same sample tube, and even
better, the same data
set, would eliminate this extra unknown.

It doesn't necessarily eliminate the unknown, it may just keep you
from finding out about it. If you were to prepare one sample on
Monday, see significant differences, celebrate, etc and then on
Wednesday prepare another sample where you didn't you'd probably want
to know that (and figure out why). Simply taking the FACS tube off
the
cytometer and putting it back on won't give you that information.
Now,
would I be surprised if that actually happened in your case? Yes.
Would I do replicates anyway? Yes.

measured in FL1, FL2, and FL4 respectively).  We are using a
bivariate
dot plot of FL1
vs. FL4 in which we are isolating 3 subsets (R1, R2, and R3) based on
their relative
expressions of FL1 vs. FL4.  We then want to compare the MFIs, as
measured in FL2, among
these subsets.   Within those 100,000 total events, there are 500 of
R1, 700 of R2 and
1200 of R3.

stack-collected data), there will become exactly 500 events in the R2
region.  If we crop
the 100,000 total events to 40,000 total events, there will become
500
events in R3.

can directly compare MFIs among the subsets that have identical
sample
sizes.  We could
also then say that, when comparing means between these subsets under
identical
experimental conditions, Rx gives a consistently higher fluorescent
signal than Ry.

Well, depending on what you're doing (you've never said how you
intend
to compare means), equal sample sizes is not particularly required so
there's no particular reason to cut the data to obtain equal sample
sizes. For example, one-way ANOVA (or one-way ANOVA with repeated
measure in the event that you chose to do _real_ replicates), which
simply says "they're different" (there are other tests, variants of
one-sided t-tests essentially, that give you directionality
statements
such as mu_{R_1} > mu_{R_2} ). In this case your assumptions are:

1. Each group is independent
2. Normality of group populations (or at least "close enough" to
Normal)
3. The _population_ variances of the dependent variable for each
group
are equal (or pretty close). (Actually check this. It would be
unsurprising to encounter large differences in the population
variances among your different groups).

Like I say, it depends a bit on what you intend to do for your
analysis. For example, _two_-way ANOVA actually expects equal sample
sizes.

function?

On an FCS file directly? Probably not (neither the manipulation of
the
flow data nor the testing). Once you've got the data out of FCS form
and appropriately labeled with group membership or split into
separate
files or something similar, then any reasonable statistics package
(Excel is not included in the list of reasonable statistics packages)
can perform the statistical tests.

Personally, I use R (http://www.r-project.org) for analyzing all the
flow data I have, but it can be intimidating for new users (though
extremely powerful once you learn to use it). There are two packages
in R for manipulating flow data at the moment (prada and rflowcyt),
available through the Bioconductor Project
(http://www.bioconductor.org) that can actually read in and
manipulate
FCS data directly or slightly manipulated data from say FlowJo (so
you
can do your gating there for example). I'm also part of a group made
up of the people who did rflowcyt and prada that are making a
combined
package of the best bits of both (and some other new bits) that we
expect to be available in the next Bioconductor release (probably
sometime in April).

Hope that helps,

Byron

expression

plot;

same

500

sample, it

total

R2,

numbers

some

should

only

--
Byron Ellis (byron.el...@gmail.com)
"Oook" -- The Librarian
Received on Thu Feb 8 14:58:00 2007
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From: Stevan Lauriault <ste...@lauriault.com>
Date: Wed Feb 07 2007 - 10:16:03 EST
Hi and thanks,

Since we want to directly compare MFIs (in FL2) between any two
subsets (R1 vs. R3) that
are isolated on a bivariate dot plot (FL1 vs. FL4), doing so in
separate sample tubes
would introduce the extra probability of experimental error between
sample tubes.
Directly comparing the subsets from the same sample tube, and even
better, the same data
set, would eliminate this extra unknown.

Let us say we have acquired 100,000 total events (stained with 3
fluorochromes, measured
in FL1, FL2, and FL4 respectively).  We are using a bivariate dot
plot
of FL1 vs. FL4 in
which we are isolating 3 subsets (R1, R2, and R3) based on their
relative expressions of
FL1 vs. FL4.  We then want to compare the MFIs, as measured in FL2,
among these subsets.
Within those 100,000 total events, there are 500 of R1, 700 of R2
and
1200 of R3.

If we crop the 100,000 total events to 75,000 total events (from the
top in
stack-collected data), there will become exactly 500 events in the R2
region.  If we crop
the 100,000 total events to 40,000 total events, there will become
500
events in R3.

Now the three populations; R1, R2, and R3 each have exactly 500 total
events, and we can
directly compare MFIs among the subsets that have identical sample
sizes.  We could also
then say that, when comparing means between these subsets under
identical experimental
conditions, Rx gives a consistently higher fluorescent signal than
Ry.

Is this a reasonable strategy?  Is there any software available that
can perform this
function?

Kind Regards,

Stevan Lauriault

---------- Original Message ----------------------------------
From: "Byron Ellis" <bcel...@stanford.edu>
Date:  Tue, 6 Feb 2007 12:17:35 -0800

expression

plot;

same

500

it

total

R2,

numbers

only

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Re: gate-specific data cropping
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From: Byron Ellis <bcel...@stanford.edu>
Date: Tue Feb 06 2007 - 15:17:35 EST
Speaking as a statistician, I would not count running the same tube 3
times or simply cutting the FCS file (the two are equivalent) as
three
replicates so I wouldn't do either to achieve what you want (though I
can imagine situations where you would resample to calculate
statistics). To get three replicates you would have to prepare three
separate samples---you're interested in the variability of the mean
due to experimental error as well as the biological variability of
the
cells and a single sample preparation only captures the latter.

On 2/5/07, Stevan Lauriault <ste...@lauriault.com> wrote:

same

it

R2,

numbers

--
Byron Ellis (byron.el...@gmail.com)
"Oook" -- The Librarian
Received on Wed Feb 7 18:58:00 2007
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From: Eric Van Buren <eric.vanbu...@wayne.edu>
Date: Wed Feb 07 2007 - 10:57:01 EST
Stevan,

It's not exactly what you're looking for, but the easiest "off the
shelf" solution may
be to acquire time as a parameter. Or, if your software allows, use
the simulated time
parameter. Gate on time empirically to produce the the desired number
of events in
each region.

As you say, the sampling is random, so it shouldn't matter which
"time
slice" you choose.
However, to keep a uniform protocol you may want to always start your
time gate with time
equals zero, i.e. starting at the beginning of the list mode file.
This should minimize
any time-related artifacts, such as sample settling, sample/sheath
dye
equilibrium,
exposure to room light, temperature, etc.

--Eric

same

numbers

Eric Van Buren <eric.vanbu...@wayne.edu>
Manager, Flow Cytometry Core Facility
Karmanos Cancer Institute
Detroit, Michigan, USA
Received on Wed Feb 7 18:38:01 2007
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gate-specific data cropping
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From: Stevan Lauriault <ste...@lauriault.com>
Date: Mon Feb 05 2007 - 13:56:18 EST
Dear All,

Question:

We are isolating leukocyte subsets to measure and compare relative
levels of expression
of certain antigens.  For example, there are three subsets within a
bivariate dot plot;
gated on R1, R2 and R3 respectively, and we would like to
statistically analyze the
relative mean fluorescence intensities of a biomarker, among the
subsets.

To get statistically comparable sample sizes among these subsets, we
are running the same
tube three times and changing the storage criteria to 500 events for
each subset
(example, the first run is 500 events of R1, the second 500 of R2,
and
the third is 500
of R3).  Instead of repeating the same tube three times, and wasting
valuable sample, it
seems like a good idea to "crop" a preexisting data file of, for
example, 100,000 total
events, three times to get an identical sample size for all three
gated subsets (R1, R2,
and R3).

Scientifically, this shouldn't be a problem, since flow cytometry
data
is collected
randomly within the same sample tube.  Not only could we run one
acquisition to get
different monocyte subset populations, but also to statistically
compare constant numbers
of monocytes, PMNs, lymphocytes, lymphocyte subsets, etc.  However, I
can see why some
scientists might be uneasy with the idea of manipulating raw list-
mode
data.

However, Since the data is collected randomly from the same sample,
doing this should
give exactly the same readings as if we just collected less events,
since we would only
be cropping (from stack-collected data) the most recent events
collected.

Currently, we are acquiring 3 different data files for each tube, and
adjusting the
acquisition and storage settings for each acquisition.  Is there a
way
to perform a
gate-specific data cropping function with any current flow cytometry
data analysis
software?

Kind Regards,

Stevan Lauriault

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RE: DNA analysis software
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From: Novo, David <david.n...@denovosoftware.com>
Date: Fri Feb 16 2007 - 19:05:22 EST
Hello Ibtissam,

Multicycle is a very commonly used DNA analysis program. It can
automatically detect the number of aneuploid populations that you
have
(if any) and runs them through several different models with
different
fitting parameters to help you determine which is the best one for
your
data. It also has a wide range of debris and aggregate compensation
to
allow it to be used with a wide variety of sample preparation
methods.

Multicycle has just been incorporated as a plug in module to FCS
Express, so that you get the benefits of the high end DNA analysis as
well as the ease of use and gating/presentation abilities of FCS
Express. It really makes DNA analysis a snap.

There is some information available at
http://www.denovosoftware.com/site/Multicycleplugin.shtml

-Dave

-----------------------------------

David Novo

President

De Novo Software

david.n...@denovosoftware.com

________________________________

From: Ibtissam Abdul-Jabbar [mailto:iajab...@cicr.uq.edu.au]
Sent: Wednesday, February 14, 2007 8:41 PM
To: cyto-inbox
Subject: DNA analysis software

Dear All, before buying software to analyse DNA on PC, I would like
to
get your opinion. I already have ModFit for Macintosh.

What are you using and what do you recommend for research purposes.

Is MultiCycle Av the one of choice?

I appreciate your comments.

Ibtissam A Jabbar (PhD)

Manager of the FACS facilities

Diamantina Institute for Cancer, Immunology and Metabolic Medicine
(DI)

The University of Queensland

Level 4 R Wing

Princess Alexandra Hospital

Ipswich Rd Buranda QLD 4102

Australia

Ph: 07 3240 5945

Fax: 07 3240 5946

Mob: 0401154744

Received on Mon Feb 19 13:38:00 2007
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DNA analysis software
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From: Ibtissam Abdul-Jabbar <iajab...@cicr.uq.edu.au>
Date: Wed Feb 14 2007 - 23:41:15 EST
Dear All, before buying software to analyse DNA on PC, I would like
to
get your opinion. I already have ModFit for Macintosh.

What are you using and what do you recommend for research purposes.

Is MultiCycle Av the one of choice?

I appreciate your comments.

Ibtissam A Jabbar (PhD)

Manager of the FACS facilities

Diamantina Institute for Cancer, Immunology and Metabolic Medicine
(DI)

The University of Queensland

Level 4 R Wing

Princess Alexandra Hospital

Ipswich Rd Buranda QLD 4102

Australia

Ph: 07 3240 5945

Fax: 07 3240 5946

Mob: 0401154744

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FACSCalibur - developing software for Macintosh
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From: Simon Crase <Simon.Cr...@invetech.com.au>
Date: Tue Feb 13 2007 - 16:32:34 EST
I've developed software to analyze data from a FACSCalibur, and our
client has asked whether we can port it to run on the FACSCalibur
itself. I understand the FACSCalibur includes a Macintosh. I'm
interested in knowing whether anyone has done this before, especially
with Java, and what pitfalls they encountered.

Simon A. Crase

Invetech Pty Ltd
Private Bag 44
495 Blackburn Road
Mount Waverley  Vic  3149

Phone:  61 3 9211 7933
Mobile: 0424 782 725
Fax:    61 3 9211 7702 (facsimile)
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Flow analysis software
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From: Xiangle Sun <sunxian...@yahoo.com>
Date: Wed Sep 12 2007 - 17:12:44 EDT
Hi, Flowers,
We just got BD LSRII flow cytometer with FACSDiva
software. I know Flowjo is a popular software and some
people use FlowJo instead of FACSDiva to do data
analysis even it comes with instrument.
My questions are:
1. What are the advantages of FlowJo and FACSDiva.
Then is it worth of purchasing FlowJo to do analysis?
2. How about the feature of FlowJo and FACSDiva on DNA
cycle analysis?
3. Are there any other better analysis softwares?
either for multicolor phenotyping, DNA cycle or both?

Any comments that based on your experience will be
greatly appreciated!

Xiangle Sun

___________________________________________________________________________­
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RE: CFSE proliferation software
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From: user facs_copy <facs_c...@wehi.EDU.AU>
Date: Wed Sep 19 2007 - 02:03:28 EDT
Michael,

Depends what you mean by "analyze".  If you mean just to extract cell
numbers at each division state, we use our own Weasel program for
that
(see http://www.wehi.edu.au/cytometry/WEASELv2.html , scroll to the
bottom
of the page).  We also have a proliferation modelling program,
CytonCalculator, that can take that proliferation data and fit a
model
calculation to it (see
http://www.wehi.edu.au/WEHI_Groups/indexworkgroups.php?id=115 for the
entry point that describes the process).  CytonCalculator may be
downloaded free.  You'll find the download link on that page.

Frank Battye.

   |    |     < The Cytometry Laboratory
    \__/  <<<<< The Walter & Eliza Hall Institute
------!!<<<<<<<< Post Office, Royal Melbourne Hospital
    /!!\  <<<<< Victoria 3050, Australia
   o !! \     < ph: 61_3_9345 2541, fax: 61_3_9347 0852
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RE: CFSE proliferation software
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From: <moo...@mail.MED.UPENN.EDU>
Date: Mon Sep 17 2007 - 19:20:03 EDT
I also agree.  We do a lot of proliferation studies and have found
that
Proliferation Wizard on Modfit is very good.

Jonni

Quoting James F George <jgeo...@uab.edu>:

--
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RE: CFSE proliferation software
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From: James F George <jgeo...@uab.edu>
Date: Mon Sep 17 2007 - 09:37:30 EDT
I have found the Modfit software from Verity to be quite useful for
this, and it integrates with Winlist rather nicely, if you have it.
Don
at Verity has been very helpful over the years in helping us
implement
the software for routine analyses.

I highly recommend this company.

I have no financial interest in Verity.  I am just a long-time user.

James F. George, PhD  |  Professor
Division of Cardiothoracic Surgery  |  University of Alabama at
Birmingham

701 South 19th St.  |  Birmingham, AL 35294

Phone: (205) 934-4261  |  Fax: (205) 975-0085

Email: jgeo...@uab.edu <mailto:jgeo...@uab.edu>

UAB HEALTH SYSTEM
Medicine that touches the world

________________________________

From: Kalos, Michael [mailto:MKa...@coh.org]
Sent: Thursday, September 13, 2007 5:39 PM
To: cyto-inbox
Subject: RE: CFSE proliferation software

No doubt this has been brought up before:  I am looking for software
recommendations to analyze data for measuring proliferation using
CFSE.
Our data is acquired on an FC500 and our computers are PC-based.

Thanks in advance,

Michael Kalos

Michael Kalos, Ph.D.
Director, Clinical Immunobiology Correlative Studies Laboratory
Division of Cancer Immunotherapeutics and Tumor Immunology
Division of Hematology and Hematopoietic Cell Transplantation
City of Hope
1500 East Duarte Road,
Duarte, CA 91010-5004
mka...@coh.org
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Received on Mon Sep 17 14:18:01 2007
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GUAVA Files
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From: Maria Laura <mcaba...@gemabiotech.com>
Date: Fri Sep 14 2007 - 16:20:15 EDT

Hi!

I´ve run  Reticulocite samples using Guava EasyCyte Citometer . I
want
to
analyze Guava Files using Summit Software (MoFlo)  and I don´t see
the
same
Plots.

Guava saves files FCS 3.0 and 2.0 .  Summit can only read 2.0 but the
Plots
shows very different.

I´ve analyzed FCS files from other different Citometers using the
Summit
software, and never had a problem.

Is there any way to convert the files?

Thanks in advance

Laura Cabanas

Buenos Aires

Argentina

Received on Mon Sep 17 13:38:00 2007
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RE: CFSE proliferation software
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