[BioC] Problem using write.FCS in flowCore 1.11.20
Nishant Gopalakrishnan
ngopalak at fhcrc.org
Tue Sep 29 21:06:46 CEST 2009
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
>
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