aligent cgh data raed and normalized

Question

[sainiisha22]

i have aligent CGH data i have download the raw file as well as series matrix file in which they have log value but they do not have probe name.. how to read and normalized the data that is not clear with me...i have seen in limma package in that they have this command targets <- readTargets("targets.txt") RG <- read.maimages(targets, source="genepix", wt.fun=f) but i am confused what is in targets.txt file which type of data it have..

Please help me

[Benn]

I might be wrong (cause I never worked with CGH data), but are you sure you need to use limma for normalization of your CGH arrays?

If your answer is yes:

First of all:

source="genepix" should be source="agilent"

In your targets file you put info about your arrays/samples. So which sample is on which array, and what conditions/treatments/etc does this sample has. There are many examples in the manual.