[BioC] Help please: FCS binary to ascii text using bioconductor

Josef Spidlen jspidlen at bccrc.ca
Mon Apr 12 23:23:54 CEST 2010

Hi David,
the following chunk of code should do it:

FCS2CSV <- function(in.file, out.file) {
    packageExists <- require(flowCore)
    if(!packageExists) {
        stop( "Please install flowCore first.", call.=FALSE)
    myFrame <- read.FCS(in.file, transformation=FALSE)
    write.csv(myFrame at exprs, file=out.file, row.names=FALSE)

The resulting CSV is basically an ASCII encoded table with column 
headings corresponding to your FCS parameter names. Please note that 
this way you are losing the information that is stored in the keywords 
in the original FCS file. Let me know if you would like to extract these 
as well. As an alternative to BioConductor, we also have some Java-based 
command line tools that can do these conversions. Drop me an email off 
line if you could use them.

Best regards,

bioconductor-request at stat.math.ethz.ch wrote:
> ------------------------------
> Message: 17
> Date: Fri, 9 Apr 2010 09:31:39 -0700 (PDT)
> From: David Lyon <david_lyon3 at yahoo.com>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Help please: FCS binary to ascii text using
>         bioconductor
> Message-ID: <128198.38448.qm at web113509.mail.gq1.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
> Hi
> can someone let me know if flow cytometry binary files can be converted to ascii text using bioconductor?
> I have spend days looking at the tutorials and searching forums but have yet to see that this can be done?
> I have seen this done on windows based programs eg:
> http://research.stowers-institute.org/efg/ScientificSoftware/Utility/FCSExtract/index.htm
> but wanted something that works on linux and can be used high throughput.
> Thanks so much in advance for your help!

Josef Spidlen, Ph.D.
Terry Fox Laboratory, BC Cancer Agency
675 West 10th Avenue, V5Z 1L3 Vancouver, BC, Canada
Tel: +1 (604) 675-8000 x 7755

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