[BioC] RE : Error in intgroup of arrayQualityMetrics package

[Wolfgang Huber]

Dear Sonal,

you asked the same question before: 
https://stat.ethz.ch/pipermail/bioconductor/2012-June/045922.html and I 
replied, asking you for more information that is needed to diagnose your 
problem.

Now, you post this again, adding that you won't be able to provide the 
needed information. Sorry, but this means I am not able to provide help.

The 'intgroup'-related functionality in the package works, as is shown 
for several examples in the package vignette.

	best wishes
	Wolfgang



Sonal Bakiwala [guest] scripsit 06/15/2012 08:30 AM:
>
> 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