Hi, I am conducting a DESeq2 differential expression analysis for which I have 200 tumor samples and 170 of their paired normal tissues.
We intend to take them all (200) into the same article and I am wondering how can I analyze them together in a statistically acceptable way.
So far the idea is to do the 170 tumor vs 170 normal paired test (170 patients) and then a unpaired 30 tumor vs 30 normal (60 patients) test. For the unpaired analysis I would be using 30 samples taken randomly from the pool of 170, or those that are grouping near in a heatmap...does this makes sense?
Then, I would be comparing the log2foldchanges of the 200 cases together if possible in order to find subgroups.
Would this be acceptable?
Thank you for this fantastic tool.
David.