I a new comer for RNA-seq, here I have some questions for RNA-seq analysis.
I want to analyze about 10 type immune cells (more than 100 samples) and find the differential expressed genes. Now, I know that these data are from 12 different paper, I treat this as 12 batch then want to remove batch effect cause by different experiment.
Is it right for my understanding about batch effect?
Or I can do DE analysis just using TPM generated from raw counts.
Thank you, everyone!!