Problem writing large FCS files using write.FCS in flowCore 1.12.0
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@robert-bruggner-4021
Last seen 7.3 years ago
Hi all, I'm running flowCore 1.12.0 and am having trouble writing a large FCS file (1.15 million events, 39 channels) using write.FCS(). The error I am getting is: Error in rep(" ", 8 - nchar(i)) : invalid 'times' argument For example: > a = read.FCS(filename="/Users/rbruggner/Desktop/big.fcs") > dim(exprs(a)) [1] 1143353 39 > write.FCS(a,filename="/tmp/big.fcs") Error in rep(" ", 8 - nchar(i)) : invalid 'times' argument > If I create a new flowFrame with a subset of the events (say, 100k events), the write works correctly. Does anyone have any suggestions as to what might be causing this error? Many thanks for any suggestions. -Rob Attached session info: R version 2.10.1 (2009-12-14) x86_64-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] stats graphics grDevices utils datasets methods base other attached packages: [1] flowCore_1.12.0 rrcov_1.0-00 pcaPP_1.8 mvtnorm_0.9-9 robustbase_0.5-0-1 Biobase_2.6.1 loaded via a namespace (and not attached): [1] feature_1.2.4 graph_1.24.1 ks_1.6.8 MASS_7.3-5 stats4_2.10.1 tools_2.10.1
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@nishant-gopalakrishnan-3253
Last seen 7.3 years ago
Hi Rob, Thank as lot for reporting this issue. I was able to reproduce the error by creating a large flowFrame and trying to write it to an FCS file. I have checked in a fix for this issue in flowCore version 1.13.10. and should be available in a day or so via biocLite(). Nishant On 04/13/2010 06:34 PM, Robert Bruggner wrote: > Hi all, > > I'm running flowCore 1.12.0 and am having trouble writing a large FCS file (1.15 million events, 39 channels) using write.FCS(). The error I am getting is: > > Error in rep(" ", 8 - nchar(i)) : invalid 'times' argument > > For example: > > >> a = read.FCS(filename="/Users/rbruggner/Desktop/big.fcs") >> dim(exprs(a)) >> > [1] 1143353 39 > >> write.FCS(a,filename="/tmp/big.fcs") >> > Error in rep(" ", 8 - nchar(i)) : invalid 'times' argument > >> > If I create a new flowFrame with a subset of the events (say, 100k events), the write works correctly. Does anyone have any suggestions as to what might be causing this error? Many thanks for any suggestions. > > -Rob > > Attached session info: > R version 2.10.1 (2009-12-14) > x86_64-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] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] flowCore_1.12.0 rrcov_1.0-00 pcaPP_1.8 mvtnorm_0.9-9 robustbase_0.5-0-1 Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] feature_1.2.4 graph_1.24.1 ks_1.6.8 MASS_7.3-5 stats4_2.10.1 tools_2.10.1 > _______________________________________________ > 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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