[BioC] Problem using write.FCS in flowCore 1.11.20

[Nishant Gopalakrishnan]

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
>