[BioC] boxplot error with expression set using oligo package and Human gene st 1.0 arrays

[jos matejus]

Dear All,

I was wondering whether anyone could help decipher an error message I
am getting when I try to plot a boxplot of normalised expression
values using the oligo package for human gene st 1.0 arrays. Here is
the code I am using:

library(oligo)
library(limma)
library(genefilter)
library(pd.hugene.1.0.st.v1)
library(hugene10sttranscriptcluster.db)

cel.dir <- "C:/cel files"
cel.files <- list.celfiles(cel.dir, full.names=TRUE)

#construct some phenodata
theData <- data.frame(Key=rep(c("VitC", "Control"), each=3))
rownames(theData) <- basename(cel.files)

vMtData <- data.frame(channel = factor("_ALL_",
levels = c("channel1", "channel2",
"_ALL_")), labelDescription = "Sample treatment")

pd <- new("AnnotatedDataFrame", data = theData, varMetadata = vMtData)

affyData<-read.celfiles(cel.files, pkgname="pd.hugene.1.0.st.v1", phenoData=pd)

eset <- rma(affyData, target="core")

show(eset)
#ExpressionSet (storageMode: lockedEnvironment)
#assayData: 33297 features, 6 samples
# element names: exprs
#protocolData: none
#phenoData
# rowNames: RB1_A1_140, RB2_A2_14010, ..., RB6_C3_10  (6 total)
#varLabels and varMetadata description:
#  Key: Sample treatment
#  additional varMetadata: channel
#featureData: none
#experimentData: use 'experimentData(object)'
#Annotation: pd.hugene.1.0.st.v1

boxplot(eset, transfo = identity, main = "After RMA")

#Error in .local(x, ...) : object 'nsamples' not found

I noticed a similar problem was reported in the archives at:
http://thread.gmane.org/gmane.science.biology.informatics.conductor/29047/focus=29050

however, I am still receiving this error message despite using version
1.12.1 of the oligo package. I have also used:

boxplot(exprs(eset))

as suggested by Mike Smith
(http://thread.gmane.org/gmane.science.biology.informatics.conductor/29047/focus=29050)

but this seems to indicate a large number of outliers which I dont get
when plotting before normailsation and also when using the
arrayQualityMetrics package on post processed values.

arrayQualityMetrics(expressionset = eset)

Any help would be gratefully received.
Best
Jos

sessionInfo()
R version 2.11.0 (2010-04-22)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United
Kingdom.1252

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

other attached packages:
 [1] hugene10sttranscriptcluster.db_5.0.1 org.Hs.eg.db_2.4.1
        AnnotationDbi_1.10.1
 [4] pd.hugene.1.0.st.v1_3.0.1            RSQLite_0.9-1
        DBI_0.2-5
 [7] genefilter_1.30.0                    limma_3.4.1
        oligo_1.12.1
[10] oligoClasses_1.10.0                  Biobase_2.8.0

loaded via a namespace (and not attached):
[1] affxparser_1.20.0     affyio_1.16.0         annotate_1.26.0
Biostrings_2.16.2     IRanges_1.6.4
[6] preprocessCore_1.10.0 splines_2.11.0        survival_2.35-8
xtable_1.5-6