Question: Using DESeq2 to analyse TCGA data
gravatar for victor.ramos.usp
22 months ago by
victor.ramos.usp0 wrote:


I'm currently using TCGA Data in my project. I'm trying to establish a pipeline to analyse these data but I have a question regarding to some statistical problem that I am not aware of.

Before downloading the TCGA Data, I could check on TCGA website that the available data (regarding hg19 genome - I'm using data level 3) the gene counts are estimated by RSEM:

I just want to know, once these data are preprocessed using RSEM, if I can put these read counts table into DESEQ2. I wanna know either if could happen some statistical inconsistence using these data on DESeq2.

* I alread checked this posts: 

But I still confued.

Thank you all.


To download data, I'm using TCGAbiolinks as following:

if (!require("TCGAbiolinks")) {

 if (!require("SummarizedExperiment")) {


# Downloading data

query.exp.proj.gene = GDCquery(project = i,
                                         legacy = TRUE,
                                         data.category = "Gene expression",
                                         data.type = "Gene expression quantification",
                                         platform = "Illumina HiSeq",
                                         file.type = "results")

 GDCdownload(query.exp.proj.gene, directory = '~/GDCdata/')

 exp.proj.mrna = GDCprepare(query = query.exp.proj.gene, save = TRUE, save.filename = paste0(i, "-mRNA.rda"), directory = '~/GDCdata')

# Loading RDA file

 load(file = paste0('~/GDCdata/RDAFiles/', i, '-mRNA.rda'))

# Count Table \/

 exp.matrix = assay(data)





ADD COMMENTlink modified 22 months ago by Michael Love26k • written 22 months ago by victor.ramos.usp0
Answer: Using DESeq2 to analyse TCGA data
gravatar for Michael Love
22 months ago by
Michael Love26k
United States
Michael Love26k wrote:

Yes, you can import RSEM into DESeq2. You can use the tximport Bioconductor package then DESeqDataSetFromTximport, or you can just round the counts and use DESeqDataSetFromMatrix.

ADD COMMENTlink written 22 months ago by Michael Love26k
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