Question: RE : Error in intgroup of arrayQualityMetrics package
7.0 years ago by
Guest User • 12k
Guest User • 12k 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:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=C LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  BiocInstaller_1.4.6 arrayQualityMetrics_3.12.0  affy_1.34.0 limma_3.12.1  Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached):  affyio_1.24.0 affyPLM_1.32.0 annotate_1.34.0  AnnotationDbi_1.18.1 beadarray_2.6.0 BeadDataPackR_1.8.0  Biostrings_2.24.1 Cairo_1.5-1 cluster_1.14.2  colorspace_1.1-1 DBI_0.2-5 genefilter_1.38.0  grid_2.15.0 Hmisc_3.9-3 hwriter_1.3  IRanges_1.14.3 lattice_0.20-6 latticeExtra_0.6-19  plyr_1.7.1 preprocessCore_1.18.0 RColorBrewer_1.0-5  reshape2_1.2.1 RSQLite_0.11.1 setRNG_2011.11-2  splines_2.15.0 stats4_2.15.0 stringr_0.6  survival_2.36-12 SVGAnnotation_0.9-0 tools_2.15.0  vsn_3.24.0 XML_3.9-4 xtable_1.7-0  zlibbioc_1.2.0 > intgroup  "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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