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

[David]

Chao-Jen Wong <cwon2 at ...> writes:

> 
> 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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> > Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
> >   
> 

Hi Chao-Jen

Thanks for your efforts.

"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."

This is exactly what I am looking for "cytometry binary files converted to ascii
text"


does anyone know how to do this in bioconductor?


thanks everyone for their help