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At this point, the two channel data has been replaced by a single value.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





	[[alternative HTML version deleted]]

