virtualArray package - Error while combing data sets
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Last seen 6 months ago
Delaware
Hi Andreas (and everybody), I am using virtualArray package to combine Illumina and Affymetrix micro-array datasets. As mentioned in the virtualArray manual and publication I prepared 'ExpressionSet' from both affymetrix and Illumina datasets. But while compiling a 'virtualarray' I get an error. MINIMAL CODE: IL.mydata <- lumiR.batch(filelist) AF.mydata <- ReadAffy() AF.eset.BG <- bg.correct.rma(AF.mydata) IL.eset.BG <- lumiB(IL.mydata, method = c('bgAdjust.affy')) virtArrays.EB <- virtualArrayExpressionSets(all_expression_sets=c('AF.eset.BG','IL.eset .BG'),identifier = 'SYMBOL') SCREEN OUTPUT/ERROR: >virtArrays.EB <- virtualArrayExpressionSets(all_expression_sets=c('AF .eset.BG','IL.eset.BG'),identifier = 'SYMBOL') Now preprocessing raw data of AF.eset.BG : Loading annotations... Now preprocessing raw data of AF.eset.BG : Collapsing expression values to their median ... Using identifier as id variables Now preprocessing raw data of AF.eset.BG : Annotating expression values with SYMBOL ... Size of expression matrix of AF.eset.BG : 22051 rows and 31 columns Now preprocessing raw data of IL.eset.BG : Loading annotations... Now preprocessing raw data of IL.eset.BG : Collapsing expression values to their median ... Using identifier as id variables Now preprocessing raw data of IL.eset.BG : Annotating expression values with SYMBOL ... Size of expression matrix of IL.eset.BG : 19443 rows and 6 columns Matching and merging all data sets. This could take some time... Size of expression matrix of whole dataset: 16536 rows and 37 columns Now combining pData of all data sets... Now setting up pData of AF.eset.BG ... Now setting up pData of IL.eset.BG ... The file 'sample_info.txt' has been written to your current working directory. Please modify it appropriately! Using only 'Batch' column as information for batch effect removal. Reading Sample Information File Reading Expression Data File Found 2 batches Found 0 covariate(s) Found 544800 Missing Data Values Standardizing Data across genes Error in solve.default(t(des) %*% des) : Lapack routine dgesv: system is exactly singular: U[1,1] = 0 I am not being able to understand the reason behind the error and would really appreciate help on this. I have come across few potential bugs in virtualArrays pack too which I will post once done with this part. Session Info: >sessionInfo() R version 2.15.3 (2013-03-01) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lumiMouseAll.db_1.18.0 lumi_2.10.0 nleqslv_2.0 mouse4302.db_2.8.1 [5] org.Mm.eg.db_2.8.0 RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.20.7 [9] Biobase_2.18.0 BiocGenerics_0.4.0 virtualArray_1.2.1 preprocessCore_1.20.0 [13] plyr_1.8 loaded via a namespace (and not attached): [1] affy_1.36.1 affyio_1.26.0 affyPLM_1.34.0 annotate_1.36.0 [5] BiocInstaller_1.8.3 Biostrings_2.26.3 colorspace_1.2-2 gcrma_2.30.0 [9] GEOquery_2.24.1 grid_2.15.3 IRanges_1.16.6 KernSmooth_2.23-10 [13] lattice_0.20-15 MASS_7.3-23 Matrix_1.0-12 methylumi_2.4.0 [17] mgcv_1.7-23 nlme_3.1-108 parallel_2.15.3 RCurl_1.95-4.1 [21] reshape2_1.2.2 splines_2.15.3 stats4_2.15.3 stringr_0.6.2 [25] tools_2.15.3 XML_3.96-1.1 xtable_1.7-1 zlibbioc_1.4.0 Thanks A. [[alternative HTML version deleted]]
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