Problem using write.FCS in flowCore 1.11.20
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@robert-bruggner-3708
Last seen 6.0 years ago
United States
Hi all, I installed flowCore 1.11.20 from source and was attempting to read an FCS file written using the write.FCS function but have run into an error. # Read an FCS file in flowFrame = read.FCS("/tmp/sample_5_ifng_il4.fcs",transform=FALSE); # Write it to a temporary FCS File write.FCS(flowFrame,"/tmp/test.fcs"); # Read the temporary FCS File that was just written flowFrame2 = read.FCS("/tmp/test.fcs",transform=FALSE); Error in 2:(nrCols + 1) : NA/NaN argument In addition: Warning message: In read.FCS("/tmp/flow.fcs") : NAs introduced by coercion Does anyone have thoughts on what may be causing such an error? I am using Biobase_2.4.1 although I understand flowCore 1.11.20 is supposedly part of the 2.5 release and thought that this could potentially be an issue. Attached Session info: R version 2.9.2 (2009-08-24) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] flowCore_1.11.20 rrcov_0.5-02 pcaPP_1.7 mvtnorm_0.9-7 robustbase_0.4-5 Biobase_2.4.1 loaded via a namespace (and not attached): [1] feature_1.2.4 graph_1.22.5 ks_1.6.6 MASS_7.2-48 stats4_2.9.2 tools_2.9.2 Many thanks for any suggestions, -Rob
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@nishant-gopalakrishnan-3253
Last seen 7.2 years ago
Hi Robert, Would it be possible to send me the "sample_5_ifng_il4.fcs " file which produced the error. I can take a took at the issue if I am able to reproduce it on my machine. Thanks Nishant Robert Bruggner wrote: > Hi all, > > I installed flowCore 1.11.20 from source and was attempting to read an FCS > file written using the write.FCS function but have run into an error. > > # Read an FCS file in > flowFrame = read.FCS("/tmp/sample_5_ifng_il4.fcs",transform=FALSE); > # Write it to a temporary FCS File > write.FCS(flowFrame,"/tmp/test.fcs"); > # Read the temporary FCS File that was just written > flowFrame2 = read.FCS("/tmp/test.fcs",transform=FALSE); > > Error in 2:(nrCols + 1) : NA/NaN argument > In addition: Warning message: > In read.FCS("/tmp/flow.fcs") : NAs introduced by coercion > > Does anyone have thoughts on what may be causing such an error? I am using > Biobase_2.4.1 although I understand flowCore 1.11.20 is supposedly part of the > 2.5 release and thought that this could potentially be an issue. > > Attached Session info: > R version 2.9.2 (2009-08-24) > i386-apple-darwin8.11.1 > > locale: > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] flowCore_1.11.20 rrcov_0.5-02 pcaPP_1.7 mvtnorm_0.9-7 > robustbase_0.4-5 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] feature_1.2.4 graph_1.22.5 ks_1.6.6 MASS_7.2-48 stats4_2.9.2 > tools_2.9.2 > > Many thanks for any suggestions, > > -Rob > > _______________________________________________ > 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 >
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@nishant-gopalakrishnan-3253
Last seen 7.2 years ago
Hi Robert, I have just checked in some changes to fix this issue in the devel branch of flowCore. You should be able to get the updated version using biocLite tomorrow afternoon. Thanks a lot for reporting this issue . Nishant -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Robert Bruggner Sent: Tuesday, September 29, 2009 11:24 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Problem using write.FCS in flowCore 1.11.20 Hi all, I installed flowCore 1.11.20 from source and was attempting to read an FCS file written using the write.FCS function but have run into an error. # Read an FCS file in flowFrame = read.FCS("/tmp/sample_5_ifng_il4.fcs",transform=FALSE); # Write it to a temporary FCS File write.FCS(flowFrame,"/tmp/test.fcs"); # Read the temporary FCS File that was just written flowFrame2 = read.FCS("/tmp/test.fcs",transform=FALSE); Error in 2:(nrCols + 1) : NA/NaN argument In addition: Warning message: In read.FCS("/tmp/flow.fcs") : NAs introduced by coercion Does anyone have thoughts on what may be causing such an error? I am using Biobase_2.4.1 although I understand flowCore 1.11.20 is supposedly part of the 2.5 release and thought that this could potentially be an issue. Attached Session info: R version 2.9.2 (2009-08-24) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] flowCore_1.11.20 rrcov_0.5-02 pcaPP_1.7 mvtnorm_0.9-7 robustbase_0.4-5 Biobase_2.4.1 loaded via a namespace (and not attached): [1] feature_1.2.4 graph_1.22.5 ks_1.6.6 MASS_7.2-48 stats4_2.9.2 tools_2.9.2 Many thanks for any suggestions, -Rob _______________________________________________ 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
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