[BioC] How to do Affy ST array analysis

[Ninni Nahm [guest]]

Hi all!

I am feeling a little bit stupid, but I have been searching for two days now (maybe I search wrong?!) and could not figure it out.
I want to analyze a Human Gene st array. 
I know that there is the oligo package, I found this annotation package here pd.hugene.2.0.st, but, I do not know how to do the steps. I am used to the affy package and affy pipelines. 
All I find when searching for solutions are ways on how to make your own annotation package, that is not necessary, I think, because I found the pd.hugene.2.0.st. Or am I wrong? Somehow I can t use it in the same way as I do with the for example hgu133a.db package that provides me the annotations.

Im really lost... 

I want to do:

- probe level analysis (similar to affyplm)
- RMA normalization (Somehow oligo does this, I think)
- Filter probes that are controls (as one does with affy: AFFX, for hgu133a)
- annotation of probesets (normally, I would use the IQR filter to get unique entrez ids, but how do I do this with the ST array?)


I know that there is something about probe and transcript to be aware of and core? But I cannot connect the workflow. 

I would be so happy if someone helped me, pointed me to the right docs. (the oligo userguide is not so helpful for me because I still dont understand what to do with what and when...) Sorry!

Thanks!

Ninni

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