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tvpham / iq

An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
BSD 3-Clause "New" or "Revised" License
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what is the protein quantification by MaxQuant? #15

Open humility3239 opened 2 months ago

humility3239 commented 2 months ago

In the iq package, we use the following code to compare protein quantification between iq and MaxQuant? Line1: w1 <- iq::maxLFQ(pro.ID)$estimate Line2: w2 <- as.numeric(dda_log2[pro.ID2,]) Line3: w2 <- w2 - mean(w2, na.rm = TRUE) + mean(w1, na.rm = TRUE)

w1 is the estimate of protein quantification from iq, while w2 is the output from MaxQuant. My question is what does the Line3 mean? The code in Line2 shows the protein quantification from MaxQuant, why Line3?

tvpham commented 2 months ago

It is to bring the average of w2 to that of w1. Note that it is relative quantification, so adding a constant to the quantification in log space maintains the relative differences between samples.