Closed jamesbangbang1126 closed 7 months ago
Dear @jamesbangbang1126, thanks for using TrendCatcher! The ideal input for run_TrendCatcher function is the raw count table without batch effect. But if you need normalization or batch effect, you can check the source code of preprocess_TrendCatcher.R. Here we applied CPM normaliztion and ComBat_seq batch correction functions, then converted it back into integers.
Hi! guys, Thank you for your great work. However, I am a little confused if TPM or FPKM, the kind of transformed expressions, could be the input of the function, ‘run_TrendCatcher’. If not, how could I use TPM or FPKM as input?
Thank u in advance.