[BioC] agilent shRNA library
Giusy Della Gatta
gd2253 at columbia.edu
Mon Sep 13 22:23:32 CEST 2010
I have microarray data coming from a Agilent custom shRNA library (3 controls "DMSO" and 3 treatments "DBZ").
To normalize these data I used the following code:
RG<-read.maimages(targets$FileName, source="agilent", ext="txt")
By doing the correlation plot between the different samples I noticed that one sample (DBZ#1) looks weird. It seems that there is any correlation between this sample triplicates and between this sample and the control (see attachment). This is happening only with DBZ#1. On the other hand, by using GeneSpring software from Agilent this sample looks OK.
Please, someone can help me into find out which is the error that I am doing in the script?
Thank you very much,
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