Affy Mouse Transcriptome Array analysis with Bioconductor

Question

[Juan Cordero]

Dear community,

I am a newbie in Affy analysis with Bioconcuctor and, while 3'UTR arrays analysis results quite straightforward (normalisation, DE, enrichment analysis...), I am struggling when analysing mouse transcriptome array (MTA) data. I have some questions I would really appreciate to be answered by the community:

1. When I read the cel files, it tells me the annotation of the HTAFeatureSet (why is it called HTA when it should be MTA?) object is pd.mta.1.0. However, there's no pd.mta.1.0ENTREZID function to fetch the Entrez Ids from the probeset names once I normalise the raw data. How could I get that function?
2. What's the difference between normalisation with target="probeset" and target="core"?
3. When I use featureFilter function from gene filter package, it gives me null results. It seems it doesn't find any Entrez Id. How could I solve this?

I would just like to read the files, get the probesets for the exons only (ignoring splicing variants), then aggregate the probes by probesets (per gene) and then do DE analysis across 3 samples, but the oligo vignette from bioconductor is not enough to understand how to do it.

Answer 1

[cpad0112]

Considering that you are a newbie, did you try free Affymetrix transcription analysis console?
http://www.affymetrix.com/estore/catalog/prod760001/AFFY/Transcriptome+Analysis+Console+%28TAC%29+Software

[Juan Cordero]

No, I didn't, but I need to use bioconductor (I can write code in python and R, so programming is not an issue)