TCGAanalyze_DEA ERROR of TCGAbiolinks
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messimess • 0
@messimess-21955
Last seen 2.9 years ago

Dear all I'm new in R packages and got problems running TCGAanalyzeDEA of TCGAbiolinks with the following error "Error in names(x) <- value : 'names' attribute [7] must be the same length as the vector [5]". No error was reported till the TCGAanalyzeDEA functions was used. Any help will be greatly appreciated.

Here are the scripts I used: library(TCGAbiolinks) library(SummarizedExperiment) setwd("I:/Rdata/WTTARGET") queryexpWT <- GDCquery(project = c("TARGET-WT"), data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - Counts", sample.type = c("Primary solid Tumor","Solid Tissue Normal")) resultsexpWT <- getResults(queryexpWT) GDCdownload(queryexpWT, method = "client") WT.exp <- GDCprepare(query = queryexpWT, save = TRUE, save.filename = "WTExp.rda") dataPrepWT <- TCGAanalyzePreprocessing(object = WT.exp, cor.cut = 0.6) dataNormWT<- TCGAanalyzeNormalization(tabDF = dataPrepWT, geneInfo = geneInfoHT, method = "gcContent") dataFiltWT <- TCGAanalyzeFiltering(tabDF = dataNormWT, method = "quantile", qnt.cut = 0.25) dataSmTPWT <- TCGAquerySampleTypes(getResults(queryexpWT,cols="cases"),"TP") dataSmNTWT <- TCGAquerySampleTypes(getResults(queryexpWT,cols="cases"),"NT") matNT <- dataFiltWT[ ,dataSmNTWT] matTP <- dataFiltWT[ ,dataSmTPWT] dataDEGsWT <- TCGAanalyzeDEA(mat1 = matNT, mat2 = matTP, Cond1type = "Normal", Cond2type = "Tumor", fdr.cut = 0.01, logFC.cut = 1.5, method = "glmLRT", paired = FALSE)

software error • 476 views
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@kevin
Last seen 2 hours ago
Republic of Ireland

I believe this is a bug in TCGAbiolinks, as reported previously on Biostars (and addressed by me):

Exploring the issue further, I found another bug, which I mention in my answers on Biostars and reported in a GitHub issue.

By the way, you should format your code the next time by highlighting it and using the 101 010 button - Did you look at your own post after you created it?

Kevin

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