[BioC] RE : Error in intgroup of arrayQualityMetrics package

[Wolfgang Huber]

Dear Tim

thanks for spotting this. That's indeed an unintended interaction of 
this cleanUpPhenoData function (which we needed after seeing some highly 
verbose and redundant ExpressionSet objects generated from ArrayExpress) 
and the 'intgroup' functionality. As a workaround, what you suggest 
below is perfect.

Fixing this, as well as the suggestions by Daniel Aaen Hansen of 1 June, 
are on the to-do list for this summer.

	best wishes
	Wolfgang


Jun/18/12 2:01 PM, Tim Rayner scripsit::
> 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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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber