[BioC] How to get and save normalized data from limma

[Wang, Jixin]

Hi Mark,
Thank you very much for your kind reply.

I want to get normalized cy3 and cy5 channel data and tend to look at the correlation (scatter plot) of normalized data between biological replicates and dye swaps. But I can’t figure out R code for this task. I will use MeV(TM4) and Cluster/TreeView software to do the clustering.

Here is my target file:

SlideNumber	FileName	Cy3	Cy5	Date
13845971	13845971.gpr	R	wild type	8/12/2008
13845972	13845972.gpr	wild type	R	8/12/2008
13845392	13845392.gpr	R	wild type	8/12/2008
13845393	13845393.gpr	wild type	R	8/12/2008
13845400	13845400.gpr	R	wild type	8/12/2008
13845401	13845401.gpr	wild type	R	8/12/2008


Regards,

Jixin
 
----- Original Message -----
From: "Mark Robinson" <mrobinson at wehi.EDU.AU>
To: "Jixin Wang" <jixinwang at neo.tamu.edu>
Cc: bioconductor at stat.math.ethz.ch
Sent: Wednesday, September 10, 2008 5:00:23 PM GMT -06:00 US/Canada Central
Subject: Re: [BioC] How to get and save normalized data from limma

Jixin.

I believe you want the normalized log-ratios, which are stored in MA$M.

For example:

library(gplots)
heatmap.2(MA$M)

... of course, depending on the number of rows in your data, you may  
want to take a subset ...

HTH,
Mark

On 11/09/2008, at 6:27 AM, Wang, Jixin wrote:

> Dear All,
>
> I want to use the normalized signal intensities data to do  
> hierarchical clustering. But I don’t know how to save the normalized  
> data from LIMMA.
>
>
> Below is the code:
>
> library(limma)
> setwd("C:/Documents and Settings/JWang/Desktop/analysis with R/RAO")
> targets <- readTargets("equi.txt")
> targets
> RG <- read.maimages(targets$FileName, source="genepix")
> RG
>
> MA <- normalizeWithinArrays(RG)
>
> MA <- normalizeBetweenArrays(MA,method="scale")
>
> design <- c(-1,1,-1,1,-1,1)
> fit <- lmFit(MA,design)
>
>
> fit <- eBayes(fit)
> topTable(fit,number=500,adjust="BH")
>
> volcanoplot(fit)
>
> Thanks a lot,
>
> Jixin
>
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------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852

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