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

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)

 

 

 

 

ADD COMMENTlink modified 5 months ago by Michael Love19k • written 5 months ago by victor.ramos.usp0
1
gravatar for Michael Love
5 months ago by
Michael Love19k
United States
Michael Love19k 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 5 months ago by Michael Love19k
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