Question: Comparing Normal vs Tumor RNAseq data from TCGA
gravatar for ad
4.2 years ago by
United States
ad30 wrote:

Hi, I'm currently looking over RNASeqV2 Level 3 data from TCGA. I was wondering if there were any pitfalls to doing a quick and dirty comparison of the RPKM values for say matched Normal samples vs the RPKM values for matched tumor samples for x genes. Can I just compare them outright from normal set to tumor set? Does it really matter that there are more tumor samples if I simply compare them as groups?

PS I know depending on the tissue there are certain subtypes listed under the same cancer so I sometimes seperate out by that ie ductal and lobular for breast invasive carcinoma.

sequencing rna-seq gene • 2.4k views
ADD COMMENTlink modified 4.2 years ago by Sean Davis25k • written 4.2 years ago by ad30
gravatar for Sean Davis
4.2 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

The size of the groups does not matter, so if you are comfortable with using the RPKMs, then you can move forward.

ADD COMMENTlink written 4.2 years ago by Sean Davis25k
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