DepMap recently received the following question:
Since DepMap does not have gene expression data for cell lines from normal (non-cancer) tissue, I planned to use data from GTEx. However, the normalization method is different (according to GTEx), “Expression values were normalized between samples using TMM as implemented in edgeR”.
For each gene, expression values were normalized across samples using an inverse normal transform.). I need to compare gene expression between cancer cell lines and normal tissues. Is there a way to make expression data from the two sources comparable? Thanks