[BioC] limma::read.maimages on different chips

[Brent Pedersen]

Hi, I have been given a bunch of data; some of it is from a 384x164
chip and another
that is 532x85.

First question, how can I read these in and normalize them together?
I can create separate target files for each set. But then how to merge?
I have seen the limma section title 'Combine RGList, MAList, EList or
EListRaw Objects',
but since there are different rows (probes),

Second, I'm using this invocation:

 dat = read.maimages(files=dir('data/scrubbed/', full.names=T),
      annotation=c("Row", "Col", "ProbeName", "SystematicName"),
      source="agilent.median",
      green.only=T)

Is that any different from:

dat<-read.maimages(files=dir('data/scrubbed/', full.names=T),
      columns=list(
          G = "gMedianSignal", Gb = "gBGMedianSignal"),
      annotation=c("Row", "Col", "ProbeName", "SystematicName"),
      green.only=T)
?


If there's somewhere with example analyses of single channel agilent data,
please let me know. I'm going off what I found in the archives.
thanks,
-Brent