RE: FCS files and software compatability

Simon,

Along with several collaborators we are currently working on developing
specifications that will hopefully aid the analysis of data across
different software such as you are describing. Our goal is to facilitate
the interchange of flow cytometric analyses between software packages,
investigators and laboratories, including data exchange standards for
analysis (especially gating) and experimental meta data. However that
doesn't help you today. 

What should help you is that one of the co-investigators on our project
is Robert Gentleman, a co-developer of R, who is leading the work on
rflowcyt. While but we are also working on example implementations in
Java (with help from Perry Haaland's group at BD and Adam Treister's
group TreeStar), the R package is the most developed at the moment on
the analysis side. Based on Robert's work (and Tony Rossini before him)
you don't need to convert your data to text to get it into R, rflowcyt
reads FCS files directly into R data objects. Robert released an update
to rflowcyt a couple of weeks ago that you can access as part of the
BioConductor package (http://www.bioconductor.org/). This release fixes
some issues and adds further functionality. There is ample documentation
for R that you should look at first
(http://cran.r-project.org/manuals.html,
http://cran.r-project.org/other-docs.html) along with most importantly
the 61-page manual on rflowcyt itself
(http://www.bioconductor.org/docs/vignettes.html) which nicely explains
how to do this. After you have looked at all that documentation you
could also get in touch with Nolwenn LeMeur (nlemeur@fhcrc.org), who has
done much of the recent work on rflowcyt, as she is also in Seattle.

Cheers,
Ryan

Ryan Brinkman, PhD
Senior Scientist, Terry Fox Laboratory
BC Cancer Research Centre &
Assistant Professor, Medical Genetics, UBC
675 West 10th Avenue
Vancouver, BC V5Z 1L3
Tel: (604) 675-8132
http://www.bccrc.ca/tfl

-----Original Message-----
From: Mr Simon Corrie [mailto:s369338@student.uq.edu.au] 
Sent: Sunday, October 30, 2005 9:18 AM
To: cyto-inbox
Subject: FCS files and software compatability

Hi folks

Im doing a short research project in Seattle and as such will have 
data from three different machines (Moflo, LSR2, Beckman MPLFC500) and 
three different software (mainly analysis) packages (FACSDiva, Summit, 
CPX).

I am finding it difficult to analyse my data across softwares - 
generally the problem seems to relate to the high resolution of the 
FACSDiva package, such that opening data in summit or CPX gives me 
data in the very low quadrant (log) areas. To solve the problem I 
would like to find a convenient method to convert my FCS files from 
various sources into .txt files so that I can use Matlab or R to 
analyse the data.

So finally my questions are:
1) Can someone suggest a program for the batchwise conversion of FCS 
to text? (I have tried ldata, but the FCS2.0 and 3.0 files do not 
convert)

2) Can someone give me a reference to help me learn how to set up my 
statistical analysis in R? ie maybe the most recent guide to rflowcyt 
if thats what people are using or an easier method? (I can code in 
matlab.....R frankly looks scary with a lack of reference material..)

Any ideas would be much appreciated

Regards

Simon Corrie
PhD Student
Nanotechnology and Biomaterials Centre
University of Queensland
St Lucia 4072 QLD Australia