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

[Yong Li]

Dear Brent,

as no one has answered your e-mail so I will have a try.

As to your first question of how to read in and normalize data from 
different chips together, these recent posts might be of help:

https://stat.ethz.ch/pipermail/bioconductor/2011-August/040726.html
https://stat.ethz.ch/pipermail/bioconductor/2011-August/040576.html

As to your second question, by checking the source of read.maimages 
(just type read.maimages in R), there should be no difference of your 
two commands except in the second case the source in the RGlist is set 
to generic.

The Bioc package Agi4x44PreProcess works with single channel Agilent 
data. But I am not sure if it will work with 384x164 or 532x85 chips.

Best regards,
Yong

Brent Pedersen wrote:
> 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
> 
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