[BioC] Differences: mas5/mas5calls vs. call.expr/pairwise.comparison

[Benjamin Otto]

Dear BioC members,

in my last calculations I noticed that the affy-package combination of
mas5() and mas5calls() results in different Present/Absent calls than the
simpleaffy-package version with call.exprs() and pairwise.comparison(). That
was the more surprising for me as I thought simpleaffy was just some wrapper
around the affy-package automating some high-level steps. A comparison of
the results with the ones returned by the affymetrix software revealed that
the simpleaffy version is nearly identical while the affy version is
different one. Is there some error in my code?
The exact commands I used were:

x <- read.affy()

#version 1:
mas <- mas5(x,sc=sometgt)
mas.call <- mas5calls(x)

#version 2:
simplemas <- call.exprs(x,"mas5",sc=sometgt)
simplemas.cmp <- pairwise.comparison(simplemas,"treatment",spots=x)


regards
Benjamin