it is my first time to work with RNA-seq data, and with this data a differential expression analysis and co-expression network analysis should be done. Now I read in the pipeline [RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR] for differential expression analysis that at first the counts are filtered (CPM), and then normlization is done with TMM. However, for the co-expression analysis I would like to use normalized data but another filtering method. So my question is: Can I also apply the TMM normalization method to unfiltered data, and then filter the normalized data afterwards? Or do you see any problem with this/have other suggestions?
Thanks in advance!