I wonder if IRS normalisation is still valid on data with NAs (without imputation)?
In that case, to get the geometric average intensity for each protein, the below modifications will be required as following:
# make new data frame with row sums from each frame
irs <- tibble(rowSums(exp1_sl,na.rm = TRUE), rowSums(exp2_sl,na.rm = TRUE), rowSums(exp3_sl,na.rm = TRUE))
# get the geometric average intensity for each protein
irs$average <- apply(irs, 1, function(x) exp(mean(log(x),na.rm = TRUE)))
Another point I'd like to mention is when a routine IRS normalisation is applied post imputation (unlike the above case), would it be still appropriate to implement ComBat normalisation on top of IRS-normalised data?
Thanks for your advice.