[BioC] GEOquery/virtualArray package error

Nafiseh Saberian [guest] guest at bioconductor.org
Tue Apr 29 18:21:20 CEST 2014

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?


 -- 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          

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