[BioC] QC for st gene arrays

[Benilton Carvalho]

affyQCReport was designed to work with objects generated by 'affy',
not by 'oligo', AFAIK.

Try using 'affy' instead with the following annotation package:

http://www.bioconductor.org/help/bioc-views/release/data/annotation/html/mogene10stv1cdf.html

I hope to be able to add QC tools to oligo soon, but, in the meantime,
consider the option above.

b

On 7 March 2011 14:57, YBao <yb8d at virginia.edu> wrote:
> 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
> Normalizing
> 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)
>
> locale:
> [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
> tools_2.12.2
> [9] xtable_1.5-6
>
> I would appreciate any help I can get from the community.
>
> Best,
>
> Yongde
>
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