Question: Downloading HTSeq raw reads with TCGABiolinks
0
gravatar for sherajilir
25 days ago by
sherajilir0
sherajilir0 wrote:

Hello Everyone! I have been trying for a while to download BRCA RNASeq data using TCGAbiolinks package from bioconductor. I followed the protocol online and everything works perfectly till GDCprepare step, where i get an error. My code is as follows:

#BRCA HT-Seq extraction with TCGAbiolinks
library(TCGAbiolinks)
library(dplyr)
library(DT)
library(SummarizedExperiment)

#Insert the name of the project
CancerProject <- "TCGA-BRCA"

#Make the data ready for download
query <- GDCquery(project = CancerProject,
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification", 
                  workflow.type = "HTSeq - Counts")

#Get the cases for each sample
samplesDown <- getResults(query,cols=c("cases"))

#Get tumor samples
dataSmTP <- TCGAquery_SampleTypes(barcode = samplesDown,
                                  typesample = "TP")

#Get normal samples
dataSmNT <- TCGAquery_SampleTypes(barcode = samplesDown,
                                  typesample = "NT")

queryDown <- GDCquery(project = CancerProject, 
                      data.category = "Transcriptome Profiling",
                      data.type = "Gene Expression Quantification", 
                      workflow.type = "HTSeq - Counts", 
                      barcode = c(dataSmTP, dataSmNT))
#Downoad the data
GDCdownload(queryDown)

#Get the .rda file containing everything. remove directory and use the main directory automatically.
BRCARnaseqSE <- GDCprepare(queryDown, save = TRUE, 
                           save.filename = "TCGA_BRCA_gene_exp.rda",
                           summarizedExperiment = TRUE)

When i come to the last step, i get this message:

Starting to add information to samples
 => Add clinical information to samples
Error in rbindlist(l, use.names, fill, idcol) : 
  Item 2 has 57 columns, inconsistent with item 1 which has 58 columns. To fill missing columns use fill=TRUE.

I tried usinf fill = TRUE, but this argument is not accepted by the function GDCprepare.

Im using R version 3.5.3

Thanks in advance!

rnaseq tcgabiolinks • 102 views
ADD COMMENTlink modified 20 days ago • written 25 days ago by sherajilir0
Answer: Downloading HTSeq raw reads with TCGABiolinks
0
gravatar for sherajilir
20 days ago by
sherajilir0
sherajilir0 wrote:

Ok problem solved!

Seems like the package has trouble of compatibility with R3.5.3. Updated to R3.6.0 and reinstalled the package.

ADD COMMENTlink written 20 days ago by sherajilir0
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