differential gene expression analysis

Question

[ravipriya11396]

how to do differential gene expression analysis in r for TCGA data??if u knows,share me. Thanks with regards in advance.

[1769mkc]

you can use the R API that is provided by TCGA

[poisonAlien]

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

[firatuyulur]

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.

Answer 1

[poisonAlien]

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.

[hibari.kyouya]

stupid question : is that a problem running DESeq2 or edgeR on TCGA data and not having technical replicates ?

Answer 2

[ravipriya11396]

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.