[BioC] GCRMA Error

[Denise Mauldin]

Greetings all,

I'm running gcrma on arrays from GSE9171 and I'm getting the infamous
'NAs are not allowed in subscripted assignments' error.

> GSE9171_GPL570_gcrma <- gcrma(GSE9171_GPL570)
Adjusting for optical effect..............................Done.
Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm :
  NAs are not allowed in subscripted assignments
> traceback()
3: compute.affinities(cdfName(object), verbose = verbose)
2: bg.adjust.gcrma(object, affinity.info = affinity.info,
affinity.source = affinity.source,
       NCprobe = NCprobe, type = type, k = k, stretch = stretch,
       correction = correction, GSB.adjust = GSB.adjust, rho = rho,
       optical.correct = optical.correct, verbose = verbose, fast = fast)
1: gcrma(GSE9171_GPL570)
> compute.affinities(cdfname="HGU133Plus2_Hs_ENTREZG", verbose=TRUE)
Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm :
  NAs are not allowed in subscripted assignments

Is this an error in the HGU133Plus2_Hs_ENTREZG CDF from brainarray?
Is there something I can do to fix this?

Thanks,
Denise

> sessionInfo()
R version 2.9.1 (2009-06-26)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] hgu133plus2hsentrezgprobe_12.0.0 AnnotationDbi_1.6.1
[3] hgu133plus2hsentrezgcdf_11.0.1   gcrma_2.16.0
[5] Biostrings_2.12.10               IRanges_1.2.3
[7] limma_2.18.3                     affy_1.22.1
[9] Biobase_2.4.1

loaded via a namespace (and not attached):
[1] affyio_1.12.0        DBI_0.2-4            preprocessCore_1.6.0
[4] RSQLite_0.7-3        splines_2.9.1        tools_2.9.1