Differences in proteusData when using readProteinGroups with different conditions

[WackerO]

Hello there,

I was wondering if the table produced by readProteinGroups is the same across multiple conditions for the same dataset. Say in the following example:

pg1 <- readProteinGroups(proteingroups.txt, metadata1)
pg1.norm <- normalizeData(pg1, norm.fun="normalizeMedian")
tab1 <- log2(pg1.norm$tab)

pg2 <- readProteinGroups(proteingroups.txt, metadata2)
pg2.norm <- normalizeData(pg2, norm.fun="normalizeMedian")
tab2 <- log2(pg2.norm$tab)

If the only difference is that in metadata1, the condition column is e.g. "treatment" and in metadata2, it is "genotype", will this only affect the coloring of plots generated from this object (e.g. with plotSampleDistributions), or will the tables also be different? I tried this with a test dataset and the diff of the tables was empty (both before and after normalizeData), but I was wondering if this was just chance or if the tables are always unaffected by the condition column.

Many thanks!