[BioC] extracting probe intensities from ReadAffy object

John Zhang jzhang at jimmy.harvard.edu
Fri Mar 14 08:32:06 MET 2003

Is this what you want?

 tt <- matrix(1:20, ncol = 4)
 rownames(tt) <- c("mygene1", "mygene2", "somthing1", "mygene3", "somthing2")
 tt[grep("mygene*", rownames(tt)),]
>From: "Wang, Hui" <Hui_Wang at affymetrix.com>
>To: "'bioconductor at stat.math.ethz.ch'" <bioconductor at stat.math.ethz.ch>
>Date: Thu, 13 Mar 2003 18:54:53 -0800
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>Subject: [BioC] extracting probe intensities from ReadAffy object
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>Hi everybody,
>This may be a R question, I am going to ask here anyway.
>I extract the pm intensities of a ReadAffy object test:
>test.intensity is a matrix with rownames of qualifier#, where # is  a probe
>number. For example, mygene1, where mygene is the qualifier and 1 is the
>first probe for that probe set with qualifier "mygene". I can access all
>intensities by test.intensity["mygene1",]
>My question is:
>is there way to extract all probe intensities for "mygene"? can I use wild
>cards here?
>Hui Wang
>Bioinformatics, Affymetrix Inc 
>Phone: 408-731-5668(Santa Clara)
>              510-428-8546(Emeryville)
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>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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