Hi,
I have searched the forum but cannot find an answer to this question. I want to compare expression of a single gene in 3 different malignancies using TCGA RNA-seq data. I have a beautiful graph from firebrowse that looks like there will be a signficant different in expression, but I need to do the stats to prove this. What is the best way to obtain the raw data, and how should it be normalized?
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written
by
mwball00 •
2 answers
Well, it looks like one very easy way to do it is to use the Firebrowse Web-API: http://firebrowse.org/api-docs/#!/Samples/mRNASeq
Select gene of interest and cohort.
It can also be done with cBioPrtal. select the cancer types you are interested in, type in the gene name and switch to the 'expression' tab and there download the data
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