I'm trying to collect the datasets from public datasets from GEO. I found some data in fpkm and some in rpkm,tpm. My goal is to feed these data into a machine learning model, but my question is "ALL THESE DATA SHOULD BE IN A COMMON FORMAT "; to do this what's the best solution?
I have two questions:
1) To have a common unit, I should convert these data to tpm ie., fpkm,rpkm to tpm; so that all values are in same format In this case how can I do this conversion?
2) If I decide to use DESeq2 to normalize; then is it right to feed all these different file formats into DESeq2 and uniformly have deseq2 normalized values?
Please help me with this?