Question: Comparing Two Genes In An Affymetrix Microarray Dataset In R
0
gravatar for soosus
7.1 years ago by
soosus80
soosus80 wrote:

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?

ADD COMMENTlink modified 7.1 years ago by lkmklsmn930 • written 7.1 years ago by soosus80

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.

ADD REPLYlink modified 7.1 years ago • written 7.1 years ago by AndreiR260
1
gravatar for lkmklsmn
7.1 years ago by
lkmklsmn930
United States
lkmklsmn930 wrote:

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

ADD COMMENTlink written 7.1 years ago by lkmklsmn930

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.

ADD REPLYlink written 7.1 years ago by soosus80

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.

ADD REPLYlink written 7.1 years ago by lkmklsmn930
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 801 users visited in the last hour