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

[James MacDonald]

You misunderstood my post; you have to compute expression measures for
the A and B chips separately, but this does not imply that you should do
disease and control separately. Also note that what you did is exactly
equal to simply running rma, but may not be as fast. You should do
something like this:

eset <- rma(Data)
exprs2excel(eset)

Best,

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> 03/15/04 12:25PM >>>
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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