Question: Chromosomal Information For Gene List In Microarray Data
1
gravatar for aditi.qamra
6.1 years ago by
aditi.qamra260
Toronto
aditi.qamra260 wrote:

Hi,

I have an expression profile dataset with a list of genes and normalized expression data. What i want is to only look at genes on the Y chromosome.

Most of the gene annotation packages with R or otherwise look for gene ids/probe-set ID to map to chromosomal information. Can you please help me out with a way to extract chromosomal information ( preferably through an R package) with only the gene names ?

Thanks !

R microarray affymetrix • 1.7k views
ADD COMMENTlink modified 6.1 years ago by Sean Davis25k • written 6.1 years ago by aditi.qamra260
3
gravatar for Sean Davis
6.1 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

The trick is to use the "org" package for your organism. Here I show human, but you can substitute....

library(org.Hs.eg.db)
symbols = c('BRCA1','TP53','GAPDH')
select(org.Hs.eg.db,keys=symbols,cols=c('SYMBOL','CHR'),keytype='SYMBOL')

Which will return:

  SYMBOL CHR
1  BRCA1  17
2   TP53  17
3  GAPDH  12
ADD COMMENTlink written 6.1 years ago by Sean Davis25k
1

R/biomaRt is another option.

ADD REPLYlink modified 6.1 years ago • written 6.1 years ago by Neilfws48k
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