Question: Obtaining gene names for .CEL files
0
gravatar for maria.kesa
6.4 years ago by
maria.kesa30
Estonia
maria.kesa30 wrote:

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 Where To Get Cdf Files Needed To Analyze Data Obtained Via The Affymetrix Platform, but I couldn't do it. I can't figure out how to use the annotation library I found  Bioconductor (http://www.bioconductor.org/packages/release/data/annotation/ 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

gene expression R • 3.1k views
ADD COMMENTlink modified 6.4 years ago by komal.rathi3.7k • written 6.4 years ago by maria.kesa30

Can you show how the gene ids look like?

ADD REPLYlink written 6.4 years ago by komal.rathi3.7k

1000_at, 1001_at etc:-)

ADD REPLYlink written 6.4 years ago by maria.kesa30
5
gravatar for komal.rathi
6.4 years ago by
komal.rathi3.7k
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.7k wrote:

 

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.

ADD COMMENTlink modified 6.4 years ago by Istvan Albert ♦♦ 86k • written 6.4 years ago by komal.rathi3.7k

Thank you, that's perfect!!!

ADD REPLYlink written 6.4 years ago by maria.kesa30

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!

ADD REPLYlink written 6.4 years ago by maria.kesa30
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