[BioC] Limma: Question about extracting 2-channel data

[James W. MacDonald]

Hi Boris,

Does the example of how to do this in the limma User's Guide (starting 
on p. 50) not suffice?

Best,

Jim

Boris Umylny wrote:
> Thank you in advance for your help.
> 
> We are trying to use limma package to extract and normalize Agilent 2-channel data.  Our objective is to use a single 2-channel chip as 2 1-channel chips.
> 
> We attempted the following:
> 
>> library(limma)
>> targets <- readTargets("targets_file", row.names = "Name")
>> RG <- read.maimages(...)
>> RG.c <- backgroundCorrect(...)
> 
> At this point we have an RG and RG.c objects that contains information for both channels.
> 
>> MA <- normalizeWithinArrays(...)
> 
> At this point, the two channel data has been replaced by a single value.
> 
> We tried to use targetsA2C to convert to 1-channel design:
> 
>> targets.1 <- targetsA2C(targets)
>> RG <- read.maimages(targets.1 ...)
> 
> However, that simply duplicated Red and Green values.  For 3 chips we had a set of 3 red and 3 green duplicates.  So, once we get to:
> 
>> MA <- normalizeWithinArrays(...)
> 
> We have 6 values, but these 6 values are 3 sets of duplicates.
> 
> How would we go about getting a set of normalized values from each channel of a 2-channel chip using limma?
> 
> 
> Sincerely,
> 
> 
> Boris Umylny
> 
> 
> 
> 
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662