[BioC] problem with justRMA in 2.10.0
Fraser Sim
fjsim at buffalo.edu
Fri Nov 6 22:32:49 CET 2009
FYI. This problem was fixed in affy_1.24.1
-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Fraser Sim
Sent: Wednesday, November 04, 2009 9:40 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] problem with justRMA in 2.10.0
I'm getting a cryptic error message when trying to run justRMA on a folder
of files, with the file names specified in celFiles. I am not setting the
phenoData or protocolData at this point and just want the eset populated
with the default pData. This code worked fine under 2.9.2. Thanks, Fraser
Here's my code:
> library(affy)
> eset <- justRMA(filenames = celFiles)
Error in validObject(.Object) :
invalid class "AffyBatch" object: 1: sample numbers differ between
phenoData and protocolData
invalid class "AffyBatch" object: 2: sampleNames differ between phenoData
and protocolData
> all(celFiles %in% list.files())
[1] TRUE
> sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] affy_1.24.0 Biobase_2.6.0 rcom_2.2-1 rscproxy_1.3-1
loaded via a namespace (and not attached):
[1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.0
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