MSstatsTMT Global Median Normalization

[Zachary Hutchins]

Hi, 

I just wanted to confirm how the global median normalization is equalizing the medians. When equalizing the channels to the global median, is a channel being multiplied or divided by a value or is it having a value added or subtracted out of it?

Thanks,

Zachary Hutchins

[Devon Kohler]

Hi Zachary,

The channels are equalized by subtracting the differences between medians so that the channels median values align. You can see the code below for more info!

Best,

Devon

.normalizePeptides = function(input) {
    input[, MedianLog2Int := median(log2Intensity, na.rm = TRUE),
          by = c("Run", "Channel")]
    median_baseline = median(
      unique(input[, list(Run, Channel, MedianLog2Int)])[, MedianLog2Int],
      na.rm = TRUE
    )
    input[, Diff := median_baseline - MedianLog2Int]
    input[, log2Intensity := log2Intensity + Diff]
    input[, Intensity := 2 ^ log2Intensity]
    input[, Diff := NULL]