I am doing differential expression analysis for a TCGA data set. When i checked PCA separation, i got something like this, a matter i have seen in GSEA as well. Two tumor samples are not separated from the normal.
Do you think i should remove these two tumor samples completely?
Thanks in advance.
This isn't a DESeq2 question per say.
I wouldn't remove the samples but I would instead try to use some other program to estimate the purity of those samples.
I cannot do that since i cannot process the raw files due to lack of computational power. I am relying on raw counts from TCGA extracted by TCGABiolinks.
Maybe you could reach out to the data generators to ask about the samples.
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