Question: How do I map Affymetrix probe IDs to gene symbols in R?
1
gravatar for c.ryder3
2.4 years ago by
c.ryder320
c.ryder320 wrote:

I have an ExpressionSet, combArr.eset, that contains Affymetrix Human Genome U133 Plus 2.0 Array gene expression data. I also have a matrix, exprs_combArr.eset, that contains the expression data for combArr.eset. The row names for exprs_combArr.eset are the hgu133plus2 probe IDs, and the column names are the Gene Expression Omnibus sample IDs.

I'd like to change the probe IDs in exprs_combArr.eset to their corresponding gene symbols, but I'm not sure how to do this.

I've retrieved the hgu133plus2SYMBOL object from the hgu122plus2.db package, which contains the mappings between manufacturer identifiers and gene abbreviations, but I'm not sure how to use this to change the probe IDs in exprs_combArr.eset.

I'm new to R and Bioconductor, and programming in general, so any help would be appreciated. Thank you!

bioconductor R • 4.9k views
ADD COMMENTlink modified 2.4 years ago by russhh4.7k • written 2.4 years ago by c.ryder320
5
gravatar for russhh
2.4 years ago by
russhh4.7k
UK, U. Glasgow
russhh4.7k wrote:

Haha, this came up in a biofinormatics clinic I did on Friday. I've written a rather terse version of how to add gene-level annotations to an Affymetrix ExpressionSet here. You basically have to find an appropriate annotation package (probably hgu133plus2.db) and add that info to the featureData slot of your ExpressionSet (don't monkey with the probe id-rownames)

ADD COMMENTlink written 2.4 years ago by russhh4.7k

Thank you! This is really helpful!

ADD REPLYlink written 2.4 years ago by c.ryder320
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