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Question: GEOquery/virtualArray package error
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3.6 years ago by
Guest User12k
Guest User12k wrote:
Hi, I am trying to use the virtualArray package, using the example code in the Vignette document, pasted below: > library(GEOquery) > library("hgu133plus2.db") > library("hgug4112a.db") > library(virtualArray) > > GSE23402 <-getGEO("GSE23402",GSEMatrix=T,AnnotGPL=FALSE) > GSE26428 <-getGEO("GSE26428",GSEMatrix=T,AnnotGPL=FALSE) > GSE23402 <- GSE23402[[1]][,1:24] > GSE26428 <- GSE26428[[1]] > exprs(GSE23402) <- log2(exprs(GSE23402)) > exprs(GSE26428) <- (exprs(GSE26428)/20*16) > > annotation(GSE23402) <- "hgu133plus2" > annotation(GSE26428) <- "hgug4112a" > > my_virtualArrays <- NULL > my_virtualArrays$iPSC_hESC_noBatchEffect <-virtualArrayExpressionSets() This code worked until about a week ago, but recently it gives me warnings and errors. In particular, I get the following warning: > Warning message: > In download.file(myurl, destfile, mode = mode, quiet = >TRUE, method = >getOption("download.file.method.GEOquery")): downloaded >length 64514067 != reported length 200 And also this error: > Now preprocessing raw data of GSE2527: Annotating expression values with SYMBOL... > Error: 2 errors; first error: > Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a > vector type, was 'NULL' I am wondering if this issue is related to an error to the GEOquery package or the virtualArray package. Is there something wrong with my installation of R or any of my packages? Regard, Nafiseh -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-redhat-linux-gnu (64-bit) attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] hgu95av2.db_2.10.1 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 DBI_0.2-7 [5] AnnotationDbi_1.24.0 BiocParallel_0.4.1 virtualArray_1.6.0 preprocessCore_1.24.0 [9] plyr_1.8.1 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affy_1.40.0 affyio_1.30.0 affyPLM_1.38.0 BatchJobs_1.2 [5] BBmisc_1.6 BiocInstaller_1.12.1 Biostrings_2.30.1 brew_1.0-6 [9] codetools_0.2-8 digest_0.6.4 fail_1.2 foreach_1.4.2 [13] gcrma_2.34.0 GEOquery_2.28.0 grid_3.0.2 IRanges_1.20.7 [17] iterators_1.0.7 lattice_0.20-29 outliers_0.14 quadprog_1.5-5 [21] Rcpp_0.11.1 RCurl_1.95-4.1 reshape2_1.4 sendmailR_1.1-2 [25] splines_3.0.2 stats4_3.0.2 stringr_0.6.2 tools_3.0.2 [29] tseries_0.10-32 XML_3.98-1.1 XVector_0.2.0 zlibbioc_1.8.0 [33] zoo_1.7-11 -- Sent via the guest posting facility at bioconductor.org.
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