Date: Mon, 22 Jun 2009 09:51:53 -0400
From: Kaiyu Shen <ks280007 at ohio.edu>
Subject: [Bioc-devel] help with limma design
To: bioc-devel at stat.math.ethz.ch
Message-ID: <1245678713.6929.0.camel at ubuntu-desktop>
Content-Type: text/plain
Hello, folks:
I am now using limma package to analyze the two-color arrays. Here are
the six arrays that I have:
# Cy3 Cy5
Array1 MU1 WT
Array2 WT MU1
Array3 MU2 WT
Array4 WT MU2
Array5 MU3 WT
Array6 WT MU3
What I want to analyze is to study the MU1 vs WT.
I tried two analysis ways, to make it easier, I have not introduced any
pre-processing methods:
A. Just have the first two arrays for analysis
# Cy3 Cy5
Array1 MU1 WT
Array2 WT MU1
object=readTargets("limma.txt")
RG=read.maimages(object,source="agilent")
MA=normalizeWithinarray(RG)
design=c(1,-1)
fit=lmFit(MA,design)
fit=eBayes(fit)
topTable(fit)
B. I include all six arrays to have other analysis simultaneously
# Cy3 Cy5
Array1 MU1 WT
Array2 WT MU1
Array3 MU2 WT
Array4 WT MU2
Array5 MU3 WT
Array6 WT MU3
object=readTargets("limma.txt")
RG=read.maimages(object,source="agilent")
MA=normalizeWithinarray(RG)
design=cbind(mu1=c(1,-1,0,0,0,0),mu2=c(0,0,1,-1,0,0),mu3=c(0,0,0,0,1,-1))
cont.matrix=makeContrasts(mu1,mu2,mu3,levels=design)
fit=lmFit(MA,design)
fit2=contrasts.fit(fit,cont.matrix)
fit2=eBayes(fit2)
topTable(fit2,coef=1) #to get the first comparison (array1 vs array2)
However, these two methods do not give me the same results.
Would somebody give me some suggestions of these two methods?
Thank you very much