Question

flowCore read.FCS unable to read FlowJo demo data set

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Johannes Rainer ▴ 80

@johannes-rainer-3234

Last seen 9.6 years ago

dear mailing list, I tried to read the demo FCS files from FlowJo's basic tutorial ( http://www.flowjo.com/home/tutorial.html) using the read.FCS function, but I always get the following error message: > Test <- read.FCS( "Sample 2.fcs" ) Error in readFCSdata(con, offsets, txt, transformation, which.lines, scale, : Don't know how to deal with bitwidth 9 I would be grateful for any suggestions, or some hints whether this is a problem in the function, or of the data files. bests, jo my sessionInfo: > sessionInfo() R version 2.11.1 (2010-05-31) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] flowCore_1.14.1 rrcov_1.0-01 pcaPP_1.8-1 mvtnorm_0.9-92 [5] robustbase_0.5-0-1 Biobase_2.8.0 loaded via a namespace (and not attached): [1] feature_1.2.4 graph_1.26.0 ks_1.6.13 MASS_7.3-6 stats4_2.11.1 -- Johannes Rainer, PhD Applied Bioinformatics Group, Division Molecular Pathophysiology, Biocenter, Medical University Innsbruck, Fritz-Pregl-Str 3/IV, 6020 Innsbruck, Austria and Tyrolean Cancer Research Institute Innrain 66, 6020 Innsbruck, Austria Tel.: +43 512 570485 13 Email: johannes.rainer@i-med.ac.at johannes.rainer@tcri.at URL: http://bioinfo.i-med.ac.at [[alternative HTML version deleted]]

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ADD COMMENT • link updated 13.7 years ago by Nishant Gopalakrishnan ▴ 340 • written 13.7 years ago by Johannes Rainer ▴ 80

score 0 · Answer 1 · 2010-08-17

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Nishant Gopalakrishnan ▴ 340

@nishant-gopalakrishnan-3253

Last seen 9.6 years ago

Hi Johannes, This appears to be a problem in the read.FCS function. Your demo FCS files are using a bit width of 9 to represent a parameter. So far we haven?t encountered files using an odd number of bits to represent a parameter. However this appears to be valid as per the FCS standards. I will try to put in a fix for this over the next couple of days. Nishant On 08/16/2010 10:37 PM, Johannes Rainer wrote: > dear mailing list, > > I tried to read the demo FCS files from FlowJo's basic tutorial ( > http://www.flowjo.com/home/tutorial.html) using the read.FCS function, but I > always get the following error message: > > >> Test <- read.FCS( "Sample 2.fcs" ) >> > Error in readFCSdata(con, offsets, txt, transformation, which.lines, scale, > : > Don't know how to deal with bitwidth 9 > > > I would be grateful for any suggestions, or some hints whether this is a > problem in the function, or of the data files. > > bests, jo > > my sessionInfo: > > >> sessionInfo() >> > R version 2.11.1 (2010-05-31) > i386-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] flowCore_1.14.1 rrcov_1.0-01 pcaPP_1.8-1 mvtnorm_0.9-92 > > [5] robustbase_0.5-0-1 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] feature_1.2.4 graph_1.26.0 ks_1.6.13 MASS_7.3-6 stats4_2.11.1 > > > >

ADD COMMENT • link 13.7 years ago Nishant Gopalakrishnan ▴ 340

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thank you very much! On Tue, Aug 17, 2010 at 9:50 PM, Nishant Gopalakrishnan <ngopalak@fhcrc.org>wrote: > Hi Johannes, > > This appears to be a problem in the read.FCS function. Your demo FCS > files are using a bit width of 9 to represent a parameter. So far we > havent encountered files using an odd number of bits to represent a > parameter. However this appears to be valid as per the FCS standards. > > I will try to put in a fix for this over the next couple of days. > > Nishant > > On 08/16/2010 10:37 PM, Johannes Rainer wrote: > > dear mailing list, > > > > I tried to read the demo FCS files from FlowJo's basic tutorial ( > > http://www.flowjo.com/home/tutorial.html) using the read.FCS function, > but I > > always get the following error message: > > > > > >> Test <- read.FCS( "Sample 2.fcs" ) > >> > > Error in readFCSdata(con, offsets, txt, transformation, which.lines, > scale, > > : > > Don't know how to deal with bitwidth 9 > > > > > > I would be grateful for any suggestions, or some hints whether this is a > > problem in the function, or of the data files. > > > > bests, jo > > > > my sessionInfo: > > > > > >> sessionInfo() > >> > > R version 2.11.1 (2010-05-31) > > i386-apple-darwin9.8.0 > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] tools stats graphics grDevices utils datasets methods > > [8] base > > > > other attached packages: > > [1] flowCore_1.14.1 rrcov_1.0-01 pcaPP_1.8-1 > mvtnorm_0.9-92 > > > > [5] robustbase_0.5-0-1 Biobase_2.8.0 > > > > loaded via a namespace (and not attached): > > [1] feature_1.2.4 graph_1.26.0 ks_1.6.13 MASS_7.3-6 stats4_2.11.1 > > > > > > > > > > -- Johannes Rainer, PhD Applied Bioinformatics Group, Division Molecular Pathophysiology, Biocenter, Medical University Innsbruck, Fritz-Pregl-Str 3/IV, 6020 Innsbruck, Austria and Tyrolean Cancer Research Institute Innrain 66, 6020 Innsbruck, Austria Tel.: +43 512 570485 13 Email: johannes.rainer@i-med.ac.at johannes.rainer@tcri.at URL: http://bioinfo.i-med.ac.at [[alternative HTML version deleted]]

ADD REPLY • link 13.7 years ago Johannes Rainer ▴ 80