Question: Comparing normal vs tumor using RPKM data from Wanderer/TCGA
gravatar for jamie_jabalee
5.4 years ago by
jamie_jabalee0 wrote:


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 upregulated, downregulated, 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 tcga rpkm • 2.5k views
ADD COMMENTlink modified 4.4 years ago by foobarbaz0 • written 5.4 years ago by jamie_jabalee0
gravatar for Alex Reynolds
5.4 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

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.

ADD COMMENTlink modified 15 months ago by Ram32k • written 5.4 years ago by Alex Reynolds31k
gravatar for foobarbaz
4.4 years ago by
foobarbaz0 wrote:

The Wanderer tool has moved, the current URL is

ADD COMMENTlink written 4.4 years ago by foobarbaz0
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