Can i a use gene expression RNAseq FPKM data provide in https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Breast%20Cancer%20(BRCA)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443 for classification of metastasis and non metastasis sample without normalization?
1 answer
Nobody can tell you because you do not say that exactly your strategy is. Generally, FPKM is a normalized unit, but it has been shown many times before that plain FPKM, that is correction only for depth (but not composition) and length might underperform if there are a lot of DEGs between groups. Here is a writeup from the past explaining plain library size vs something more sophisticated: TMM-Normalization
A great view for what composition bias is: See StatQuest
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