Dear all, I have a bulk-rna dataset which I have analyzed by DESEQ2 and I have batch corrected it using limma package and removeBatchEffect() function. I would like to calculate the FPM value for expression data through fpm() function of deseq2. I know it will use the raw data to calculate these value. I have created a heatmap from my batch corrected data for some genew and I wanted to also plot the fpm value for these genes but then due to the fact I mentioned, the activity of my genes from heatmap in each condition will not exactly correspond to their expression from FPM table. How one should deal with this problem? can I also correct the FPM data for batches? What would be the appropriate way?
Thanks a lot!