datasets comparison
Can I compare two datasets with the same platform both mononuclear cells but one of them has purified CD34+ cells?
GSE17480 vs GSE38987
leukemia
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Can you explain what you're trying to do in more detail?
I want to compare gene expression of two subtypes of leukemia
If the datasets are divided by leukemia subtype (samples of each subtype found in only one of the two sets), there is no way to differentiate biological factors from experimental and other random/human factors. You can compare them, sure, but you cannot generate any hypothesis about the cause of any differences you see.
what if I wanted to find similarities between the DGE of the two? can I develop an assumption on that?
No. I should have been clearer - you cannot generate any hypothesis based on any observation you make.