I try to remove the batch effect using Combat-seq in RNA-seq count data. Should I normalize RNA-seq raw count data before or after using the Combat-seq? Show me the example code of how to use Combat-seq and Normalization.
Also remember that standard methods like DESeq2, edgeR etc. can handle batch effect very well. You do not have to perform batch correction using outside softwares if you are planning to perform differential expression analysis using these methods.