[BioC] Limma: How to analyze 1- and 2- colour Agilent

[Edwin Groot]

Hello all,
I have a special Agilent 4x44 K microarray analysis problem.
There are 4 replicates of 2-colour arrays comparing two cell types.
I want to add to this 4 replicates each of 3 other cell types, but they
are 1-colour hybridizations (array design is the same).
How should I do the preprocessing?

My instinct is to normalizeWithinArrays() the 2-colour data, then
coerce these to single-channel (an EList?). Next background-subtract
the 1-colour data into an EList. Next, combine these two objects and
normalizeBetweenArrays(), if necessary. Finally, model and extract
contrasts.

The alternative was to fool Limma into reading red and green channels
of the 2-colour data into an EListRaw, combining with the 1-colour
data, and normalizeBetweenArrays(). However, that omits the
normalizeWithinArrays().

TIA,
Edwin

FWIW:
> sessionInfo()
R version 2.11.1 (2010-05-31) 
i486-pc-linux-gnu 

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
    

other attached packages:
[1] limma_3.4.2

loaded via a namespace (and not attached):
[1] tools_2.11.1

Dr. Edwin Groot, postdoctoral associate
AG Laux
Institut fuer Biologie III
Schaenzlestr. 1
79104 Freiburg, Deutschland
+49 761-2032945