[BioC] Problems with gcrma using latest version of R and Bioconductor

[James W. MacDonald]

Hi Sebastian,

Please always give us the output of sessionInfo() as well. Just telling 
us you have BioC 2.0 isn't sufficient. For instance, I get this to work:

 > dat <- ReadAffy(filenames=list.celfiles()[1:5])
 > eset <- gcrma(dat)
Adjusting for optical effect.....Done.
Computing affinities.Done.
Adjusting for non-specific binding.....Done.
Normalizing
Calculating Expression
 > eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 45101 features, 5 samples
   element names: exprs
phenoData
   rowNames: Kretzler 730.CEL, Kretzler 731.CEL, ..., Kretzler 734.CEL 
(5 total)
   varLabels and varMetadata:
     sample: arbitrary numbering
featureData
   featureNames: 1415670_at, 1415671_at, ..., AFFX-TrpnX-M_at (45101 total)
   varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation [1] "mouse4302"
 > sessionInfo()
R version 2.5.1 (2007-06-27)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "datasets"
[7] "utils"     "methods"   "base"

other attached packages:
mouse4302probe   mouse4302cdf          gcrma    matchprobes           affy
       "1.16.0"       "1.16.0"        "2.8.1"        "1.8.1"       "1.14.2"
         affyio        Biobase       rcompgen
        "1.4.1"       "1.14.0"       "0.1-13"

Sebastian Bauer wrote:
> Hello,
> 
> I have some problems with the gcrma normalization procedure. Please look 
> at the output:
> 
> ----
> 
> 
>  > Chips.norm<-gcrma(Chips.raw)
> Adjusting for optical effect............................Done.
> Computing affinities.Error in get(x, envir, mode, inherits) : variable 
> "mouse4302dim" was not found
>  > traceback()
> 9: get(nam)
> 8: get("NROW", get(nam))
> 7: xy2indices(p$x, p$y, cdf = cdfpackagename)
> 6: inherits(x, "factor")
> 5: is.factor(x)
> 4: match(xy2indices(p$x, p$y, cdf = cdfpackagename), pmIndex)
> 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(Chips.raw)
> 
> ----
> 
> I'm using R Version 2.5.1 and Bioconductor 2.0. I've reinstalled all 
> needed packages, but I noticed no difference in the behavior. The same 
> procedure worked with previous versions of R and Bioconductor though. 
> It's possible to circumvent the problem?
> 
> On reply, please CC me as I'm not subscribed to the list.
> 
> Thanks in advance!
> 
> Bye,
> Sebastian
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623