Question

TCGAanalyze_DEA ERROR of TCGAbiolinks

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messimess • 0

@messimess-21955

Last seen 5.1 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 • 1.7k views

ADD COMMENT • link updated 2.1 years ago by Majd • 0 • written 5.1 years ago by messimess • 0

score 1 · Answer 1 · 2019-10-04

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Kevin Blighe ★ 4.0k

@kevin

Last seen 36 minutes 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

ADD COMMENT • link 5.1 years ago Kevin Blighe ★ 4.0k

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Hi Kevin,

I realize this was a few years ago now, but I'm stuck on the same error. I went through your responses on Biostars, but I'm still confused.

Firstly, I'm trying to load data I downloaded from cbioportal. I have 2 RNA expression data frames (rna.normal.4 and rna.4), one for normal breast samples and one for tumour samples. I formatted the data frames so that the row names is the gene ID, and the columns are the RSEM counts for each sample.

When I run:

dataDEGs <- TCGAanalyze_DEA(
  mat1 = rna.normal.4,
  mat2 = rna.4,
  Cond1type = "normal",
  Cond2type = "tumor",
  fdr.cut = 0.01 ,
  logFC.cut = 1,
  method = "glmLRT"
)

I get the following error:

Error in names(x) <- value : 
  'names' attribute [7] must be the same length as the vector [1]

The dimensions of the data frames are as follows:

> dim(rna.normal.4)
[1] 20489   114
> dim(rna.4)
[1] 20489  1082

Is the error appearing because there are more tumor samples than normal? That can't be right, as it's very common for there to be more samples in one case compared to another.

The error appears whether I set PAIRED=TRUE or FALSE.

I would really appreciate your help!

ADD REPLY • link 2.1 years ago Majd • 0