Question: Affy Mouse Transcriptome Array analysis with Bioconductor
gravatar for peter pfand
5.0 years ago by
peter pfand100
peter pfand100 wrote:

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.



ADD COMMENTlink modified 5.0 years ago by cpad011214k • written 5.0 years ago by peter pfand100
gravatar for cpad0112
5.0 years ago by
cpad011214k wrote:

Considering that you are a newbie, did you try free Affymetrix transcription analysis console?

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by cpad011214k

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

ADD REPLYlink written 5.0 years ago by peter pfand100
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