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

[Adaikalavan Ramasamy]

The rownames of HGU-133A and HGU-133B are not unique (there is about 100+
redundancies). You might want to add these codes before rbind() to avoid any
confusion later.

A <- exprs(exprSetA)
rownames(A) <- paste("A.", rownames(A))
B <- exprs(exprSetB)
rownames(B) <- paste("B.", rownames(B))

Also, doing normalization before summary is better because we have more
information to utilize at probe level.


> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of James
> MacDonald
> Sent: 15 March 2004 14:11
> To: lxu at chnola-research.org; 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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