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Question: Unknown failure in virtualArrayLoadRaw
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3.6 years ago by
Guest User12k
Guest User12k wrote:
Hello everyone, I've tried to use the virtualArray-Package with this http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22153 rawfile and this code: path<- "/path/to/GSE" setwd( path ) virtualArrayDirs() vArray <- virtualArrayLoadRaw(root_dir = path) eSet <- virtualArrayCompile(virtualArray=vArray) The output: Created directory tree in /path/to/GSE/ . Please copy your raw data files into the appropriate directories. Now starting to compile "sample_info.txt" for later use with the "virtualArrayComBat" function to remove batch effects. The file "sample_info.txt" has been written to /path/to/GSE/ . Please edit the "Covariate 1" column to your needs and save before proceeding. Starting to load raw data files stored in /path/to/GSE/ . This could take some time, please be patient. All raw data has been loaded. Error in evalas.name(names(sort(sapply(X = ls(envir = virtualArray, pattern = "annot_"), : error in evaluating the argument 'expr' in selecting a method for function 'eval': Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 'x' must be atomic Is this a bug ? Greetings, Robert -- output of sessionInfo(): > sessionInfo() R version 3.0.3 (2014-03-06) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] 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 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] mogene10stv1cdf_2.13.0 hgu133plus2cdf_2.13.0 affy_1.40.0 GEOquery_2.28.0 virtualArray_1.6.0 preprocessCore_1.24.0 [7] plyr_1.8.1 BiocInstaller_1.12.1 AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affyio_1.30.0 affyPLM_1.38.0 Biostrings_2.30.1 DBI_0.2-7 gcrma_2.34.0 grid_3.0.3 IRanges_1.20.7 lattice_0.20-29 [9] outliers_0.14 quadprog_1.5-5 Rcpp_0.11.1 RCurl_1.95-4.1 reshape2_1.4 RSQLite_0.11.4 splines_3.0.3 stats4_3.0.3 [17] stringr_0.6.2 tools_3.0.3 tseries_0.10-32 XML_3.98-1.1 XVector_0.2.0 zlibbioc_1.8.0 zoo_1.7-11 -- Sent via the guest posting facility at bioconductor.org.
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