Using DESeq2 to analyse TCGA data
1
0
Entering edit mode
@victorramosusp-15032
Last seen 3.8 years ago

Hi,

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")) {
     source("https://bioconductor.org/biocLite.R")
     biocLite("TCGAbiolinks")
     library("TCGAbiolinks")
 }

 if (!require("SummarizedExperiment")) {
      source("https://bioconductor.org/biocLite.R")
      biocLite("SummarizedExperiment")
      library("SummarizedExperiment")
   }

i = "TCGA-LUSC"

# 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/')

 setwd('~/GDCdata/RDAFiles')
 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)

 

 

 

 

deseq2 tcga tcgabiolinks gene expression differential expression • 3.0k views
ADD COMMENT
1
Entering edit mode
@mikelove
Last seen 2 hours ago
United States

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 COMMENT

Login before adding your answer.

Traffic: 269 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6