[BioC] AffyBatch to ProbeSet? SpikeIn and Hgu-133?

[James W. MacDonald]

Mohammad Esad-Djou wrote:
> Hello, 
> 
> 1. I would like to convert Hgu-133 experiment from AffyBatch to ProbeSet.  Is it possible ?  If yes, how?

Well, if you mean the ProbeSet class, then you would use the probeset() 
accessor function. If you simply want all the probes for each probeset 
in e.g., a list, you would use probes(abatch, LISTRUE=TRUE). Note that 
you will have to extract the PM and MM data separately.

> 
> 2. Relationship between SpikeIn and Hgu-133 is unclear to me.  Can someone explain to me? Is there literature in addition?
> 

The HG-U133A is an Affymetrix chip whereas the Spike-in could be one of 
two experiments that were run by Affymetrix using HG-95A and HG-U133ATAG 
chips. I doubt that answers your question, but I am not sure exactly 
what you are trying to determine. Can you rephrase the question?

Best,

Jim


> Thanks,
> Mohammad Esad-Djou
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
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