[BioC] questions about Affy package from new user: onemore question

[Lizhe Xu]

Hi, Jim

Thank you very much for your help. But I still have a question, I have two groups, say disease vs control, each has three U133 set. I did rma on two group separately:
 (like what the affyDemo did on the Dilution data)
> DIS<- expresso(Data[1:3], bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish")
> CON<- expresso(Data[4:6], bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish")

>NORMTOL<-merge(DIS, CON)*

For me, it seems I still need to do sth to normalize data between two groups. 
Maybe, what I did was wrong, I should do rma on both group together.

*Also, I can do exprs2excel on DIS and CON files but not on NORMTOL. What I should do to export NORMTOL?
So far, I combined DIS and CON in Excel.

Thanks.

Lizhe


-----Original Message-----
From: James MacDonald [mailto:jmacdon at med.umich.edu]
Sent: Monday, March 15, 2004 8:11 AM
To: Lizhe Xu; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] questions about Affy package from new user: onemore question


AH. GS==GeneSpring.

If you want to join them before importing to GeneSpring, you should do
this after computing expression values. You can do something like:

out <- rbind(exprs(exprSetA), exprs(exprSetB))
write.table(out, "Combined expression data.txt", sep="\t", quote=F,
col.names=NA)

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Lizhe Xu" <lxu at chnola-research.org> 03/14/04 06:20PM >>>
Now, I tried to load the exported data from Bioconductor to GeneSpring
and found another question. Since I used U133 chip set, I wonder if I
can joint the U133A and B directly and import them to GS or I should do
probeset level normalization first (if so, which package in bioconductor
can do it) before joint them. Thanks.
 
Lxu

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