Error in IRS calculations in "understanding_IRS"

[Arthfael]

Dear Phil,

I just wrote an implementation of IRS right now for one of my pipelines and I was checking for reference your code at: https://pwilmart.github.io/IRS_normalization/understanding_IRS.html I think there is a mistake, line:

irs <- tibble(rowSums(exp1_sl), rowSums(exp2_sl), rowSums(exp3_sl))

should be

irs <- tibble(apply(exp1_sl, 1, function(x) exp(mean(log(x)))),
              apply(exp2_sl, 1, function(x) exp(mean(log(x)))),
              apply(exp3_sl, 1, function(x) exp(mean(log(x)))))
      

that is, you want an average value, and more generally, the same averaging function used to calculate irs$average should be used. Otherwise, and unless I am missing something here (but it is very simple arithmetic, and the concept is very simple and clear), the calculations do not seem to make sense: we want to correct, row-wise, for each TMT batch by the ratio between the general dataset's average and the average of all of the batch's channels (or reference channels if there are any). Best,

Armel