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

[Benilton Carvalho]

Dear Jos,

thanks for the report. I've just fixed the "object 'nsamples' not
found" error on oligo version 1.12.2, which should be available for
download in about 1 day or so.

In the meantime, the plot you want to look at is:

tmp = exprs(eset)
tmp = as.data.frame(tmp)
boxplot(tmp, range=0)

best,

b

On 7 June 2010 10:04, jos matejus <matejus106 at googlemail.com> wrote:
> 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
>
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