Question: How to do Affy ST array analysis
5.5 years ago by
Guest User • 12k
Guest User • 12k wrote:
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 -- output of sessionInfo(): - -- Sent via the guest posting facility at bioconductor.org.
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