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Question: Help please: FCS binary to ascii text using bioconductor
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gravatar for David Lyon
7.6 years ago by
David Lyon320
David Lyon320 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!
ADD COMMENTlink modified 7.6 years ago by Josef Spidlen140 • written 7.6 years ago by David Lyon320
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gravatar for Chao-Jen Wong
7.6 years ago by
Chao-Jen Wong580
USA/Seattle/Fred Hutchinson Cancer Research Center
Chao-Jen Wong580 wrote:
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! > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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
ADD COMMENTlink written 7.6 years ago by Chao-Jen Wong580
0
gravatar for David Lyon
7.6 years ago by
David Lyon320
David Lyon320 wrote:
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! > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at ... > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > 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
ADD COMMENTlink written 7.6 years ago by David Lyon320
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gravatar for Josef Spidlen
7.6 years ago by
Josef Spidlen140
Josef Spidlen140 wrote:
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, Josef 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 http://www.terryfoxlab.ca/people/rbrinkman/josef.aspx
ADD COMMENTlink written 7.6 years ago by Josef Spidlen140
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