Does anyone have any insight or experience into whether FPKM/TPM expression should be corrected for batch effect? I have come to notice that batch correction is mostly applied to raw counts and is mainly for the purpose of between-sample comparisons or visualisation. However, since FPKM and TPM are mainly used for within sample comparisons, is there a need to batch correct the expression values for samples from different batches? I guess the bigger question is whether within-sample comparison is effected by batch effect. Thanks.