Two case, Two control RNA-seq
I have a scenario where I have RNA-seq files for young control patients, young disease patients, old control patients, and old disease patients. I want to first compare disease to control for each age, to account for (normalize) transcriptional differences related to age. Then I want to compare young and old disease to see if the disease is different for younger/older patients. I am having a hard time figuring out how to do this computationally. Any suggestions?
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eshelmanm10 •
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Have you generated read count tables?
Yes. I used HTSeq to get read counts and put them in a table.
Bioconductor RNA-seq workflow: gene-level exploratory analysis and differential expression
But two vs two comparisons is statistically invalid. The bare minimum is 3 vs 3 and even then you'll have unreliable results. You'll find more technical noise than biological meaningful results.
These are just broad groups. We have >10 samples in each category.