Hi,
I have been doing pathway analysis with fgsea package but I have a question that don't understand.
I tried both DESeq and wilcoxon to get the input stats for fgsea. With DESeq I used the stats column and with Wilcoxon I used auc scores. In Wilcoxon test the output table gives a group column in which the two comparison groups are listed. Normally based some tutorials we should extract each group and do pathway analysis separately, and the auc scores are all positive. Whereas with DESeq, since the results for two groups are mixed and the gene regulations in each group are shown with positive/negative stats values, we do not need to divide the output by group but can directly use the stats column, with positive and negative values mixed.
I was wondering could this make some difference in the pathway analysis results? Which one (DESeq or Wilcoxon) is recommended?
Thanks!
