[BioC] split arrays

[scholz@Ag.arizona.edu]

Gordon,

Recently you advised someone with a split set of maize arrays that they could do
their analysis by reading all the A slides into an RGList and normalizing, then
doing the same with the B slides, and then combining the two datasets via
rbind() of the two MAList objects. I have a similar (the same?) set of arrays
and some of the users of these arrays have noted that the A and B slides perform
differently, i.e. more background on the B slide, for whatever reason. Though
I'm not actually convinced this is true, it makes me wonder whether the two
datasets should be combined at all since there may be a "between array set"
source of variation. Am I right to segregate these sets or is there some
overwhelming benefit to combining them? I'm no statistician and would appreciate
your take.

Thanks,

Matt

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