I couldn’t find this explicitly stated in the documentation:
I presume for pathway abundances, it allowed genes with identified functions to be assigned to > 1 pathway, and therefore the quantification is somewhat overlapping?
How could you take this into consideration with analysing results statistically? (I’d love to correlate differences in pathway abundance with a continuous metadata variable I have for the samples).
I used limma-trend on logCPM values calculated from the RPK values for analysing gene family abundance. Is this suitable, or would a different method be preferable
All help is much appreciated