Entering edit mode
Hi Group,
When I try to run frma() using brainarray cdfs I get an error (the
chips are HG-U133A):
> affy.batch <- ReadAffy(cdfname="hgu133ahsentrezg")
> eset.frma <- frma(affy.batch)
Error in rcModelWPLM(y = x1, w = w.tmp, row.effects = pe.tmp,
input.scale = x4) :
row.effects should sum to zero
I can run frma() without specifying a custom CDF, and rma() with the
brainarray CDF, which suggest to me that the problem isn't with the
data, frma(), or the brainarray CDF itself. When I try
"median_polish" or "weighted_average" options for summarize I get an
ominous warning instead of an error:
> eset.frma <- frma(affy.batch, summarize="median_polish")
Warning message:
In log2(pms) - input.vecs$probeVec :
longer object length is not a multiple of shorter object length
I get similar errors/warnings when I use 'AffyBatchExample' from
'frmaExampleData':
> library(frmaExampleData)
> data(AffyBatchExample)
> AffyBatchExample@cdfName
[1] "HG-U133A"
> affy.batch <- AffyBatchExample
> affy.batch@cdfName <- "hgu133ahsentrezg"
> eset.frma <- frma(affy.batch, summarize="median_polish")
Warning message:
In log2(pms) - input.vecs$probeVec :
longer object length is not a multiple of shorter object length
One thing to note is that I'm running R2.15.2 and when 'AnnotationDbi'
is loaded a warning is generated:
Warning message:
package 'AnnotationDbi' was built under R version 2.15.3
I would update to R 2.15.3 but naively I don't know if this will cause
problems with any other packages that I've installed.
Here is my sessionInfo:
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United
States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] affy_1.36.1 Biobase_2.18.0 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] affyio_1.26.0 BiocInstaller_1.8.3 preprocessCore_1.20.0
tools_2.15.2 zlibbioc_1.4.0
Any suggestions/help would be much appreciated!
Ty M. Thomson, Ph.D.
Senior Computational Biologist
Selventa
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