[BioC] bg.correct.mas

[Dennis Kostka]

hi,
i'm confused about one line in the bg.correct.mas function (file 
bg.Affy.chipwide.R, line 11). there it says:

	ally <- c(pm.index, mm.index) %/% nrow(object) + 1

to calculate the y-coordinates of the pmormm probes, i persume.
now i.e.

	(640*640) %/% 640  +1 = 641

-->	should'nt it rather be something like 
	ally <- (c(pm.index, mm.index) -1) %/% nrow(object) + 1 ?

also i'm not sure if  x and y are swapped, but of course this is of no concern 
calculating the background.
a second thing is, that the 'non pm or mm probes' are not used. can maybe 
someone give me a hint where to find out what they actually are (grid 
alignment checkerboards, text, center cross or something like this??) . the 
reason for the question is, that respecting the 'nonpmormm's i observed a 
lower mean background estimate.

thnx,
dennis

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