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Comparing normal vs tumor using RPKM data from Wanderer/TCGA

Hi,

I am trying to do a rough analysis of a certain gene in various cancer types using data I downloaded from TCGA through Wanderer. The RNA seq data is provided as log2RPKM values. What I want to do is, for my gene of interest, pair up the RPKM values of normal and tumor samples from the same patient and use a simple test (for example, fold change >=|2|) to determine if the gene is up-regulated, down-regulated, or unchanged in each individual patient. The problem is that I have done some reading and am confused on whether this type of analysis makes sense with RPKM values. I am completely new to TCGA/bioinformatics so any advice is greatly appreciated!

Thanks very much in advance.

rna-seq rpkm tcga
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updated by Ram Ram • written by jamie_jabalee • jamie_jabalee

2 answers

If helpful, I wrote a TCGA expression browser that shows normalized TPM data values for ~20k genes and 31 tissues. You can select genes and tissues of interest to render box plots. The notched boxes draw a 95% CI around the median to allow comparison between normal and tumor condition and might suggest another approach. TPM measurements try to get around some of the normalization issues with RPKM data.

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updated by Ram Ram • written by Alex Reynolds Alex Reynolds

The Wanderer tool has moved, the current URL is http://maplab.cat/wanderer/

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written by foobarbaz • foobarbaz

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