Comparing Two Genes In An Affymetrix Microarray Dataset In R

Question

[soosus]

I'm working with an Affymetrix rat transcriptome in R and would like to compare, say, expression levels of MAOA and MAOA versus a housekeeping gene like ACTB. I've gone through the basic initial stages:

rawdata = ReadAffy()
eset = rma(rawdata)

and am aware of the affy and limma packages but not entirely sure how to go about specifying only two or three genes for analysis/comparison. Help?

[AndreiR]

I dont know if I understand correctly. I think you first must to annotate. Maybe http://www.bioconductor.org/help/workflows/annotation-data/ could help. After that, I think you can use http://bioconductor.org/packages/release/bioc/html/affycomp.html.

Answer 1

[lkmklsmn]

Simplest way: A T-test between expression values of MAOA vs ACTB should tell you if there is any difference.

[soosus]

That doesn't help me in this context. I don't know how to select specific genes from an Affymetrix-type dataset. Once selected, sure, a basic t-test or regional ANOVA will be fine, but I can do neither of those things until I can specify the genes I'm interested in.

[lkmklsmn]

Oh ok.As far as I know the AffyBatch objects do not contain the gene symbol annotations.You will need to use some annotation file to map TranscriptClusterIDs to gene symbols. You could use Bioconductor packages to do that or download annotation data directly from Affy.

In your case exprs(eset) should give you an expression matrix where the rows are the probesets and the row names are the TranscriptClusterIDs.