[BioC] Problem using write.FCS in flowCore 1.11.20

Nishant Gopalakrishnan ngopalak at fhcrc.org
Wed Sep 30 01:21:11 CEST 2009

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 .


-----Original Message-----
From: bioconductor-bounces at 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
# 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
2.5 release and thought that this could potentially be an issue.

Attached Session info:
R version 2.9.2 (2009-08-24) 


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  

Many thanks for any suggestions,


Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
Search the archives:

More information about the Bioconductor mailing list