[BioC] RE : Error in intgroup of arrayQualityMetrics package

[Tim Rayner]

Hi Sonal,

You could try rearranging pData(eset) so that the "Tissue" column is
the first column, or within the first few columns. There's some
preprocessing code in the arrayQualityMetrics:::cleanUpPhenoData
function which limits the number of columns which will be carried
forward into the QC (maxcol=10). Also, the contents of the "Tissue"
column must not be either all the same or all different (a quite
reasonable requirement).

Cheers,

Tim


--
Tim Rayner
Bioinformatician
Smith Lab, CIMR
University of Cambridge


On 15 June 2012 07:30, Sonal Bakiwala [guest] <guest at bioconductor.org> wrote:
>
> I am using arraQualityMetrics package installed from Bioconductor site and R version that I am using is 2.15.0
>
> The input for the function was eset and for the intgroup argument character vector "Tissue". There is a
> column named Tissue in my phenoData of the eset.
>
> But it still gives me an error saying the elements of intgroup do not match the column names of the pData(eset).
> I don't know what wrong I am doing.
>
> The error look like this :
>
> Error in prepData(expressionset,intgroup=intgroup):
> all elements of 'intgroup' should match column names of pData(expressionset)
>
>
>
>  -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.4.6        arrayQualityMetrics_3.12.0
> [3] affy_1.34.0                limma_3.12.1
> [5] Biobase_2.16.0             BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.24.0         affyPLM_1.32.0        annotate_1.34.0
>  [4] AnnotationDbi_1.18.1  beadarray_2.6.0       BeadDataPackR_1.8.0
>  [7] Biostrings_2.24.1     Cairo_1.5-1           cluster_1.14.2
> [10] colorspace_1.1-1      DBI_0.2-5             genefilter_1.38.0
> [13] grid_2.15.0           Hmisc_3.9-3           hwriter_1.3
> [16] IRanges_1.14.3        lattice_0.20-6        latticeExtra_0.6-19
> [19] plyr_1.7.1            preprocessCore_1.18.0 RColorBrewer_1.0-5
> [22] reshape2_1.2.1        RSQLite_0.11.1        setRNG_2011.11-2
> [25] splines_2.15.0        stats4_2.15.0         stringr_0.6
> [28] survival_2.36-12      SVGAnnotation_0.9-0   tools_2.15.0
> [31] vsn_3.24.0            XML_3.9-4             xtable_1.7-0
> [34] zlibbioc_1.2.0
>> intgroup
> [1] "Tissue"
>> str(intgroup)
>  chr "Tissue"
>
> Sorry I wont be able to provide you with the detailed information of the pData.
> But the colnames(pData(eset)) has one of columns named as "Tissue" and the class of the this column is factor.
>
> Thank you.
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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