Batch effect

[sfdycod]

Hello,

For some reason,my RNA-seq data(TPM and FPKM)came from different batches,so my question is:
1 Do I need remove batch effect when I use xcell
2 If needed ,Whether negative values are permitted in the matrix which was removed batch effect by SVA

Thank you in advance!

[dviraran]

Hi,

1. xCell uses the ranking of genes, and batch effect removal won't change that, so it will have no effect.
2. Again, its all based on ranking. The values don't matter.

Best,
Dvir