combat-seq input

[saicharanp18]

Hi, Thanks for the updated combat-seq. i am trying to use combat-seq on my rnaseq data. Do i need to input raw counts or normalized counts or log transformed counts. because for combat we prefer log transformed counts.

Thanks, sai

[zhangyuqing]

Hi @saicharanp18,

Please input only raw counts without normalization or log transformation. ComBat-Seq is designed for integer count data, and will provide adjusted data as integer counts. Let me know if you have any questions.

Yuqing