Answer 2 out of 2
 
16 answers

Purdue Cytometry Mail List, Isac congress, Flow jo, Verity, J Paul Robinson

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A:

RE: commercial announcements

From: Dr. Robert Ashcroft (cytomat@netcore.com.au)
Date: Tue Jan 05 1999 - 02:04:46 EST

Dear Bill,

As an academic with commercial connections, I have found that it works if

you do either of two things:

Invite the interested parties to request you reply with a file attached to

their responding email, or simply send an attached file in the original

mailout.

 

Most people favour the first, as there are lots of people who resent the

attachment file in the primary mailouts.

 

In the second case, from the marketing viewpoint... the problem is adding

enough detail (without over-sell) in the List message to motivate the

target persons to request the file, yet not enough to alienate the set of

people who are anti-commercial

 

Hope this helps

 

-----Original Message-----

From:   Bill Throndset [SMTP:bthrondset@rigelinc.com]

Sent:   Thursday, December 31, 1998 1:40 PM

To:     Cytometry Mailing List

Subject:       commercial announcements

 

 

Personally, I usually don't mind the commercial comments, but there have

been a few that seem to have crossed the line.

 

 

I would suggest requiring a response in which a company directs readers

to products from their company as a solution to a specific cytometry

related problem to include (parenthetically) a warning such as

"propaganda" or "commercial" or "advertisement" with the subject line of

their response. For example; <bold>Subject: re CD34 staining

(commercial).

 

 

</bold>For a message from a company which is not a response for help, but

more directly an advertisement, the subject line of the email would also

include "propaganda," or "commercial" or "advertisement."  In this case,

most of us could happily delete the message before reading it!

 

 

Maybe it's just me, but I like the paradox of a salesperson typing

"propaganda" as the subject of a listserver posting.

 

 

 

 

 

 

 

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

 

bill throndset

 

bthrondset@rigel.com

 

Rigel, Incorporated

 

408-617-8106

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The "perfect" software ... also does ratios... and calibrated parameters...

From: Mario Roederer (Roederer@Stanford.edu)
Date: Fri Jun 18 1999 - 11:30:12 EST

  • text/enriched attachment: stored

·         <bold>Keri Tate</bold> asks: ·           ·           ·         >>>>  ·           ·         <excerpt>>We have recently purchased a used Coulter XL Epics (1994, 3 ·         color).  I am trying to find an efficient ·           ·         way to analyze data (particularly in messy spleen cell populations). ·         Since we have an older model computer (486-66 DTX) with little memory ·         we would like to transfer the data and analyze it on a more powerful ·         PC. <bold>  My question is what software would you suggest?</bold> ·         Although we are not a clinical lab we still do many of the same ·         experiments multiple time and would like to save template layouts.  My ·         experience is with CellQuest but recently we have being evaluating ·         "WinMDI".  My impression thus far is that although the graphics are ·         beautiful and the price is right,  it is tedious to crank through data, ·         i.e. there are several steps needed to generate one graph and one must ·         do this over and over.  Am I missing something?  What other software ·         would be useful to evaluate? ·           ·         </excerpt><<<<<<<< ·           ·           ·           ·         At Stanford, we designed FlowJo for precisely this purpose:  analyzing ·         entire experiments at a time, using "template" analyses.  It's batch ·         capabilities are particularly easy to use:  you can have it determine ·         which sets of gates & statistics to apply to which samples based on the ·         staining panels (and other criteria); it can then generate complete ·         graphical or layout reports.  Graphics are publication quality: we've ·         gone straight from FlowJo output to manuscript submission (although ·         usually we use Canvas or other drawing packages to do combine with ·         other graphic outputs).  ·           ·         See <<http://www.treestar.com/flowjo/platforms/> for some information. ·           ·           ·         FlowJo is commercially available through Tree Star ·         (<<http://www.treestar.com/flowjo>), but you can evaluate it free for ·         60 days...  I highly suggest running through the tutorial, which leads ·         you through this kind of analysis. ·           ·         And.... <bold>Chuck Radford</bold> asks ·             ·         >Does anyone out there know how to calculate the ratio ·           ·         >of fluorescence to FALS of each cell and collect it ·           ·         >as a histogram using CellQuest?  I know that Cicero ·           ·         >software is capable of doing that, but I'm not sure ·           ·         >if CellQuest can do that. ·           ·         FlowJo also computes arbitrary ratios (and can convert log <<-> linear ·         if desired).  The derived parameter can be used as any other parameter: ·          for displays, gating, statistics, and so on. ·           ·         Finally, <bold>Bill Hyun</bold> asked about calibration: ·           ·         First you need a calibration standard (there are two ways to go: ·         either use calibrated bead sets, available from a variety of ·         manufacturers, or use an anti-CD4 with a known F/P ratio and stain ·         human PBMC; CD4 T cells have 50,000 molecules of CD4 per cell (25,000 ·         antibody binding sites)).  Once you have collected a calibration ·         standard, either beads or cells, FlowJo will use this information to ·         create a derived parameter that expresses binding in terms of absolute ·         number of molecules per cell.  See <<http:// ·         www.treestar.com/flowjo/platforms/calibration.pdf>. ·           ·           ·         mr

 

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Re: Ratio calculation

From: Tree Star (treestar@professionals.com)
Date: Wed Jan 13 1999 - 19:11:06 EST

I haven't done it, but you should be able to fake a compensation matrix that will add FL1 + FL2, then derive a ratio using that new one.    We considered and dismissed the generalized parameter calculator from FlowJo because no one had (previously) expressed the need.  If your colleague can explain why that helps, and it makes sense for others, then we'll support it.   There is a problem that FCS files don't have negative numbers in them, so a general algebraic parser wont work.   Adam   On Wed, 13 Jan 1999, Joseph Webster wrote:   > > Hi All, > A slightly curly request.... :~? > > A colleague wants the ratio of (FL2 / (FL1 + FL2)) from many flow readings. > (He explained why, but I didn't understand...) > > He wants this from many datafiles, so batch processing probably.... > He wants to export this into some other program such as Excel..... > > Several computer packages can produce simple ratios of one parameter > over another, but someone is always wanting more... > > Any ideas? > > Another challenge for Ray Hicks, Adam Treister, Joe Trotter Et Al ;~) > How about the ability to enter a user-defined function or formula to be > applied to the data? > > (The "massaging" possibilities are amazing!-) > >       Thanks, Joseph. > > -- > Joseph Webster > Flow Cytometry Facility > Centenary Institute >

This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:36:52 EST

Re: Cell Cycle Analysis Software-FlowJo

From: Mario Roederer (roederer@stanford.edu)
Date: Fri Feb 12 1999 - 00:05:01 EST

>Does anyone know of any good cell cycle analysis software?

>We are currently moving from the HP workstation to the

>Macintosh workstation, and find that Modfit is a very

>poor software application. We really liked CellFit for the HP, but

>BD doesn't do Cell Cycle analysis software anymore, since they

>can't make any money at it.  We've also heard of Phoenix flow

>systems MacCycle.  We were just wondering if there were any

>others on the market besides those two applications.  Any

>help is greatly appreciated.  Thank You.

> 

 

FlowJo, originally developed here at Stanford, now comes equipped with an

integrated cell cycle platform.  It fits both Watson's "Pragmatic" model as

well as the Dean-Jett model (with the Fox modification).  Using an

interactive interface, you can put constraints on many of the fitting

parameters, allowing you to model most DNA distributions.  However, there

is currently no way to model debris background subtraction (a process which

is controversial), nor can it model cell divisions (using dyes like PKH-26

or the like).  In other words, it's not as sophisticated as ModFit, also

available for the Mac, but suffices for probably 90% of the users out there!

 

FlowJo integrates this platform into the unique drag-and-drop interface

that lets you apply your customized models to entire experiments in a

matter of seconds, create graphical reports in which you include

statistics, keyword information, and so forth.  You can even create

template analyses, so that subsequent experiments can be analyzed just by

loading the data into the workspace.

 

For more information, see the FlowJo web site:

 

www.treestar.com/flowjo

 

mr

This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:36:56 EST

Re: Data Analysis Software

From: Adam Treister (adam@treestar.com)
Date: Thu Mar 18 1999 - 00:00:08 EST

----->>>>> On 17-Mar-1999, Ray Hicks wrote: >   The reason for deconvolution is to create a perfect world >   where those assignments can be made.  The conspiring spread >   functions are modelled  and how well the model's output >   matches the real histogram is a measure of perfection.  But >   the nature of modelling still doesn't allow you to identify a >   cell. >   >   Jill wanted exact boundaries that she could gate on, I don't >   see how modelling could give them.  It identify a point where >   there is a satisfactory tradeoff between contamination from >   an unwanted compartment and loss of the required one, but >   would it improve the analysis of her horseshoes where she >   already has an indicator of S-phase? --------------   Doesn't this argument come down to a differentiation between a sort gate and an analysis gate?  At collection time, you don't want to be making decisions about an individual cell, but in post hoc analysis, there is potentially interesting information to be gleaned from looking at the overlap population, or from subtracting it out.   We've been debating this issue internally.  I think it makes sense statistically, and am lobbying for it in the next FlowJo.  Mario is the self imposed guardian of scientific rigor and likes to hold his breath until he turns blue.  But for me, the role of data analysis software is to enable exploration and to test potential models, not only to churn existing models. Mark's message lists valid uses for the capability. Clearly there are limitations, but this is flow, so what else is new?  The software is there only to calculate the numbers; it's up to the biologist to make sense of them.   Adam   ----------------------------------- Adam Treister adam@treestar.com 650-508-9349 http://www.treestar.com -----------------------------------

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Re: Macs, BD and applications & instruments

From: Adam Treister (adam@treestar.com)
Date: Mon Apr 26 1999 - 19:57:36 EST

 

Re: formula log to linear??

From: Mario Roederer (Roederer@drmr.com)
Date: Wed Jun 30 1999 - 12:55:10 EST

>Hello to All, >  >There is a simple formula for converting log data to linear, and I have >forgotten.  If anyone remembers this I would appreciate a quick note. >Thanks. >  >Jim Phillips >University of Miami School  of Medicine >Miami, Fla.   Scale (linear) Value = f * 10^ [(C * n) / R]   where   C = channel number n = number of decades for the full range (~4 on BD & Cytomation machines, ~3 on many Coulters) R = range (maximum number of channels; typically 1024) f = log offset (typically 1 or 0.1)   The FCS keyword $PxE (x = parameter number) has the values for f and n (e.g., <$P4E = 4,0.1>  means that parameter 4 has a 4 decade range with the linear scale value of channel 0 equal to 0.1); $PxR has the value for R. Note that for most BD-generated FCS files, the offset for all log parameters is incorrectly stored in the FCS keyword list as 0 (zero); it should be 1.0.   mr

This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:37:14 EST

Re: DNA analysis softwares

From: Adam Treister (adam@treestar.com)
Date: Thu Jun 10 1999 - 22:43:01 EST

----->>> On 10-Jun-1999, Ng Bee Ling wrote: >   I am looking for a software so as to determine the  % of cell cycle >   phases (with gating properties) from listmode files. Is there such >   software that could run both for files collectd from EXPO and >   Cellquest? --------------   FlowJo in an offline analysis package that will read both EXPO (PC) and CellQuest (Mac) files.   You can compute the percentages in each of the phases (as well as under-G1 and over-G2) for any gated population.   We currently have a limitation in the ability to export all of the cell cycle statistics for all of the samples to a spreadsheet in a single step, but that is implemented in the next release.   More info at: http://www.treestar.com/flowjo/html/cellcycle.html   I get a lot of requests for the references to the models, so let me give them here:   1) Watson Pragmatic Cytometry 8:1-8 (1987) Watson, Chambers, & Smith:  A Pragmatic Approach to the Analysis of DNA Histograms with a Definable G1 Peak   2) Dean Jett Fox Cytometry 1:71-80 (1980) Fox:  A Model for the Computer Analysis of Synchronous DNA Distributions Obtained by Flow Cytometry   3) Two Populations Uses Dean-Jett model (with Fox modification) for both populations.   Adam   ----------------------------- Adam Treister adam@treestar.com http://www.treestar.com/flowjo 800-366-6045 -----------------------------

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Re: Cost-benefit ratio of FlowJo [Clarification]

From: Adam Treister (adam@treestar.com)
Date: Wed Aug 04 1999 - 16:28:49 EST

If I may clarify...   Judging from the phone calls I'm getting, Cariappa may have implied that FlowJo is a cross-platform package. I think he meant that FlowJo reads data collected on any cytometer, whether it was hooked to HP, PC or Mac.  FlowJo itself still runs only on the Mac.    This may be unclear, because we are running a Summer $99 promotion, in conjunction with DeNovo Software.  They sell the PC based analysis package: FCS Express.  So, the solution I can offer you for Windows is at:    <http://www.denovosoftware.com/> The promotion is a good deal on either platform.   We are working on Win-FlowJo, but it's not close to ready. The bad news: there is no announced release planned for a Windows product in the foreseeable future.  The good news:  more for the Mac is coming pretty soon.   Adam   ----->>> On  4-Aug-1999, Cariappa Annaiah wrote: >   >   I routinely obtain flow data from both Mac and PC based >   machines and so have some experience using Mac/PC data >   analysis software. I have always found it a pain to switch >   from Mac based software to PC based software and vice versa. >   That pain is history with FlowJo! The cross-platform >   capability and the ability to do in-depth, multi-tube >   analysis has made FlowJo an important member of my pantheon >   of FCM data analysis software. Now that it is being offered >   at a really low price for a limited time (as a promotion), >   the cost-benefit ratio for FlowJo becomes very favourable, >   compared to extant FCM software. Check it out at the >   following URL: http://www.treestar.com/flowjo/summer99.html --------------     ----------------------------- Adam Treister adam@treestar.com http://www.treestar.com/flowjo 800-366-6045 -----------------------------

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New Mac Analysis Software Launch

From: Ray Hicks (rh208@cus.cam.ac.uk)
Date: Thu Aug 26 1999 - 17:59:38 EST

This is to announce the release of FCSPress, a new program for the analysis of flow cytometric data on the macintosh.   Its particular strengths are high quality graphs, on-the-page editing and annotation, intuitive (to me at least ;-) interface, copy and paste of graphics and text into other programs (at full resolution - not just bitmap or screen dump), and ease of use.   You can download a thirty day fully working demo from   http://www.fcspress.com   or   http://www.angelfire.com/biz2/rayh   (the ink hasn't had a chance to dry on the www.fcspress.com address, and it may not be recognised everywhere on the internet yet).   This release is for powermacs only, a "fat" version for non-powermacs is in the pipeline.   If you have trouble obtaining a demo from the web, you can request a copy from request@FCSPress.com <mailto:request@FCSPress.com>.   Pricing for perpetual licence, no time limit, valid for all versions 1.x:   Type                   Initial                cost           extra copies                        quantity Single                 1              $149 (99 pounds)      $149/£99   "Departmental"         5              $749 (495 pounds)      $99/£60   "Institutional"        20             $2095 (1395 pounds)    $45/£30   For further details see the manual on the web page e-mail sales@FCSPress.com <mailto:Sales@FCSPress.com>.   All orders received before 14 September 1999 receive a 25% discount, as do cheque-with-order payments in sterling drawn on a UK bank for single user licences.   Ray

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