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

	[[alternative HTML version deleted]]

