[BioC] expression levels of individual probes

[James W. MacDonald]

Hi Chris,

If you want probe level expression values, you will need to extract 
those data from your AffyBatch (probably best after background 
subtraction and normalization).

You can extract e.g., the PM probe values for AFFX-CreX-5_at using the 
pm() accessor function:

pm(abatch, "AFFX-CreX-5_at")

HTH,

Jim


Chris Dawson wrote:
> Hi there,
> I have a number of short RNAs that have high homologies to a number  
> of  individual probes in the Medicago Affymetrix Genechip (http:// 
> www.affymetrix.com/products/arrays/specific/medicago.affx).  I'd like  
> to be able to see for a few hundred probes which individuals, for  
> example Medicago:AFFX-CreX-5_at:587:698, have high fluorescence  
> levels and which do not. I realise binding efficiencies differ for  
> individual probes, but I am only looking for indicative data. Sorry  
> if I am not clear with proper terminology, I've only worked with pre- 
> made gcrma processed data sets before, not individual probes.
> Cheers,
> Chris
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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