virtualArray package
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Hi, I am very interested in using the virtual array package and have been trying it out. However, i have been getting this error (see below) even with the test data in the paper. Could you kindly advise please? -- output of sessionInfo(): > my_virtualArrays$iPSC_hESC_noBatchEffect <- virtualArrayExpressionSets() Now preprocessing raw data of GSE23402: Loading annotations... Usinghgu133plus2as Bioconductor annotation package for datasetGSE23402. Loading required package: hgu133plus2.db Loading required package: AnnotationDbi Loading required package: GenomeInfoDb Loading required package: org.Hs.eg.db Loading required package: DBI Now preprocessing raw data of GSE23402: Collapsing expression values to their median... Using identifier as id variables Now preprocessing raw data of GSE23402: Annotating expression values with SYMBOL... Now preprocessing raw data of GSE26428: Loading annotations... Usinghgug4112aas Bioconductor annotation package for datasetGSE26428. Loading required package: hgug4112a.db Now preprocessing raw data of GSE26428: Collapsing expression values to their median... Using identifier as id variables Now preprocessing raw data of GSE26428: Annotating expression values with SYMBOL... Error: 2 errors; first error: Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL' For more information, use bplasterror(). To resume calculation, re-call the function and set the argument 'BPRESUME' to TRUE or wrap the previous call in bpresume(). First traceback: 22: virtualArrayExpressionSets() 21: lapply(all_expression_sets, virtualArrayBuildfData, collapse_fun = collapse_fun, identifier = identifier) 20: lapply(all_expression_sets, virtualArrayBuildfData, collapse_fun = collapse_fun, identifier = identifier) 19: bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM) 18: bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM) 17: bplapply(X = X, FUN = FUN, ..., BPRESUME = BPRESUME, BPPARAM = SerialParam(catch.errors = BPPARAM$catch.errors)) 16: bplapply(X = X, FUN = FUN, ..., BPRESUME = BPRESUME, BPPARAM = SerialParam(catch.errors = BPPARAM$catch.errors)) -- Sent via the guest posting facility at bioconductor.org.
Annotation Preprocessing hgu133plus2 hgug4112a • 747 views
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