[BioC] QC for st gene arrays

YBao yb8d at virginia.edu
Mon Mar 7 15:57:42 CET 2011

Dear All,

I was trying to do a QC report for oligo generated mouse st gene array
data, but was met with the errors:

> library(affyQCReport)
> library(affydata)
> geneCore <- rma (affyGeneFS, target="core")
Background correcting
Calculating Expression
> featureData(geneCore) <- getNetAffx(geneCore, "transcript")
> QCReport(geneCore, file="YuMGSt6QC.pdf")
Error in box(...) : invalid 'which' argument
In addition: Warning messages:
1: In plot.window(...) : "which" is not a graphical parameter
2: In plot.xy(xy, type, ...) : "which" is not a graphical parameter
3: In axis(side = side, at = at, labels = labels, ...) :
  "which" is not a graphical parameter
4: In axis(side = side, at = at, labels = labels, ...) :
  "which" is not a graphical parameter

And, this happened after a recent updating of the R and BioC:

> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] pd.mogene.1.0.st.v1_3.0.2 oligo_1.14.0
oligoClasses_1.12.2       RColorBrewer_1.0-2        geneplotter_1.28.0
 [6] annotate_1.28.0           annaffy_1.22.0            KEGG.db_2.4.5
            GO.db_2.4.5               RSQLite_0.9-3
[11] DBI_0.2-5                 AnnotationDbi_1.12.0
affyQCReport_1.28.1       lattice_0.19-13           simpleaffy_2.26.1
[16] genefilter_1.32.0         limma_3.6.9
affyPLM_1.26.0            preprocessCore_1.12.0     gcrma_2.22.0
[21] affydata_1.11.10          affy_1.28.0
Biobase_2.10.0            R.utils_1.5.7             R.oo_1.7.4
[26] R.methodsS3_1.2.1

loaded via a namespace (and not attached):
[1] affxparser_1.22.1 affyio_1.18.0     Biostrings_2.18.2 grid_2.12.2
     IRanges_1.8.9     splines_2.12.2    survival_2.36-1
[9] xtable_1.5-6

I would appreciate any help I can get from the community.



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