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Obtaining gene names for .CEL files

Hello everybody,

My question is: how do I get a gene list using Bioconductor from a .CEL file for the HG_U95Av2 array(from the arrays at http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=75)?

I tried following the answer in this post, but I couldn't do it. I can't figure out how to use the annotation library I found in Bioconductor look for gahgu95av2)

I already figured out how to do normalization of the files using justRMA, now I need the gene annotations for the numbers.

Your hints and and answers would be really helpful:-) Thank you!

Cheers,
Maria

r gene-expression
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updated by Ram Ram • written by maria.kesa • maria.kesa

Can you show how the gene ids look like?

• 0 views • link
written by komal.rathi komal.rathi

1 answer 

source("http://bioconductor.org/biocLite.R")

biocLite("hgu95av2.db")

library(hgu95av2.db)

Annot = data.frame(SYMBOL=sapply(contents(hgu95av2SYMBOL), paste, collapse=","), 
           DESC=sapply(contents(hgu95av2GENENAME), paste, collapse=","),
           ENTREZID=sapply(contents(hgu95av2ENTREZID), paste, collapse=","),
           ENSEMBLID=sapply(contents(hgu95av2ENSEMBL), paste, collapse=","))

Annot$SYMBOL will contain the gene names for your IDs.

• 0 views • link
updated by Ram Ram • written by komal.rathi komal.rathi

Thank you so much, Komal:-) I never had a bioinformatics course or worked with Bioconductor, so I was really confused:-) Thank you for your time!

• 0 views • link
written by maria.kesa • maria.kesa

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