Hi, You could use the s apply function to create a data frame of the annotation. If hgu133 plus 2.0 is your chip something like the following could be employed
>myAnnot <- data.frame(ACCNUM=sapply(contents(hgu133plus2ACCNUM), paste, >collapse=", "), SYMBOL=sapply(contents(hgu133plus2SYMBOL), paste, collapse=", >"), +DESC=sapply(contents(hgu133plus2GENENAME), paste, collapse=", ")); or >ID <- featureNames(eset) >Symbol <- getSYMBOL(ID, "hgu133plus2.db") >tmp <- data.frame(ID=ID, Symbol=Symbol, Name=Name, Ensembl=Ensembl, >stringsAsFactors=F) >tmp[tmp=="NA"] <- NA # The stringsAsFactors makes "NA" characters >fData(eset.norm) <- tmp Regards, Ekta -----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Peter Langfelder Sent: 03 April 2012 23:00 To: email mail Cc: r-help@r-project.org Subject: Re: [R] how to map microarray probe to gene, homology On Tue, Apr 3, 2012 at 7:21 AM, email mail <email8...@gmail.com> wrote: > Hi: > > I have clustered microarray gene expression data and trying to map between > microarray probe, gene, pathway, gene ontology, and homology for a set of > (affy) microarray probes. Is there any package in R which facilitates this? > I am looking at bioconductor, but till now could not find a solution. A > link to some worked example would be appreciated. Yes, Bioconductor has annotation packages for microarray chips plus other packages for connecting gene identifiers to (for example) gene ontologies. For example, the package hgu133plus2.db contains annotations for the U133 plus 2 chip and you can use to map affy probe IDs to gene symbols, IDs, GO terms etc. Install the package, load it, then type ls("package:hgu133plus2.db") and look at the help files for each topic for more details and examples. The array annotations are chip-specific so you need to choose the right package for your chip. Peter ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a! nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
