I just started working with data from the Affymetrix GeneChip Mouse Gene 1.0 ST Array and I have two questions about that and hope that somebody can help me.
1) The first is a more general and probably very easy question but I was wondering which IDs I should use to map Affymetrix probesetids or transcriptclusterids to genes. I found here a lot of questions and very good answers about that several probesetids/transcriptclusterids are matched with the same gene etc. I don't have a problem using different R packages (biomaRt, xmapcore, mogene10sttranscriptcluster.db etc.) to match the IDs from Affymetrix to Gene Symbol, Ensembl, Entrez Gene, Unigene IDs etc. But my question is which of these IDs I should use to determine that two (or more) transcriptclusterids are matched to the same gene? In other words, what ID "type" is the standard to say that two probesets are assigned to the same gene?
I guess for most of the genes it shouldn't make a difference which ID type I use but for some probesets the annotation is different and the probesets with missing annotations are different for the different types. I saw that others used the Gene symbols (what I would have used) but I also saw the use of Unigene IDs...
2) I am using R and used ReadAffy to get an AffyBatch object from the cel files that I got from GEO. On GEO the platform is described as [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version].
From Affymetrix I downloaded two annotation files: MoGene-10-st-v1.na30.mm9.transcript.csv and MoGene-10-st-v1.na30.mm9.probeset.csv
I now wanted to match the data in my AffyBatch object to the probesetids in the probeset annotation file. When I try probeName(AffyBatch), I get the transcriptclusterids for each row in the intensity matrix (these are equal to the probesetids in the transcript annotation file) but not the probesetids from the probeset annotation file. Is the information about the probesetids from the probeset annotation file not stored in my AffyBatch object because the cel files are from a "transcript (gene) version" or what do I do wrong?
Thank you very much for your help!