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

[Chao-Jen Wong]

Hi, David,

Bioconductor has a set of packages allowing you to analysis flow
cytometry data.  flowCore is the main package that provides the data
structure and basic infrastructure to deal with flow cytmotry data. The
function "read.FCS" allows you to read FCS files  and returns an object
of class 'flowFrame' or 'flowSet'.  Function 'exprs' allows you to
extract the flow data of the 'flowFrame' or 'flowSet' objects.   There
are many functions allows you to extract the parameters once the data is
converted to 'flowFrame' or 'flowSet'.  You can then write a script to
write these data (flow data and parameters) to a txt file.  If you are
asking for a single, easy function that directly converts a .FCS file to
an ascii file with a certain format, I don't have an answer for that.


Chao-Jen

On 04/09/10 09:31, David Lyon wrote:
> 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!
>
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-- 
Chao-Jen Wong
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M1-B514
PO Box 19024
Seattle, WA 98109
206.667.4485
cwon2 at fhcrc.org