how to do differential gene expression analysis in r for TCGA data??if u knows,share me. Thanks with regards in advance.
•
written
by
ravipriya11396 •
Maybe try something like this. Assuming you have two groups, first download rnaseq-counts for barcodes in these two groups. Below change TCGA cohort name to yours.
group1 = TCGAbiolinks::GDCquery(project = "TCGA-ESCA",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - Counts", barcode = group1Barcodes)
TCGAbiolinks::GDCdownload(query = group1, directory = 'group1_counts')
group2 = TCGAbiolinks::GDCquery(project = "TCGA-ESCA",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - Counts", barcode = group2Barcodes)
TCGAbiolinks::GDCdownload(query = group2, directory = 'group2_counts')
This will get you raw counts. You can use either DESeq2 or EdgeR to perform DE analysis. See their respective vignettes for usage.
stupid question : is that a problem running DESeq2 or edgeR on TCGA data and not having technical replicates ?
I had retrived clinical data and made it as two groups each group has barcode with their status based on some criteria.now i want to do differential gene expression analysis for those particular barcodes alone.if you know please share me. Thanks with regards in advance.
Log in to answer this question.
you can use the R API that is provided by TCGA
What have you tried so far ? Its hard to guide you with this limited information. Do you have datasets from TCGA to analyse ? Look at bioconductor package like TCGABiolinks
If you are allowed to download the data, do a featureCounts on .bam files and do a DESeq2, both on R. Their vignettes are very user friendly and they have their R script in their Bioconductor website. see http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html and https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/Rsubread.R for the pdfs and R scripts.