[BioC] raw probe set expression data and masking questions

[Schwartz, Donald]

Anyone know a simple method to harvest the raw probe set level expression data (not individual PM probe or PM-MM probe pair level data), which will be summarized by average difference, and then export that into excel with the Affy ID or "probe set name" as row headers and columns representing samples? 
 
Second question, I have a small affy custom array. I want to select certain probe sets for analysis prior to any low-level processing (i.e., prior to normalization and background correction, etc.). In other words, I want to mask certain probe sets before normalization and background correction. Following masking, the probe sets will be ignored for the entire analysis. The difficulty is that there is no consistent naming feature across all probe sets so the only way to identify probe sets to mask or to analyze is with a character vector. In addition, I need the flexibility to mask different sets of probe sets and then process (normalize, bg.correct, etc) the data various ways. I'll use: expresso(affybatch, widget=TRUE) to do this post masking.  
 
Thanks for your suggestions.
Don
 

Donald R. Schwartz, PhD
Research Scientist
Karmanos Cancer Institute

Wayne State University School of Medicine

6137 Scott Hall
540 E. Canfield
Detroit, Michigan 48201
(313)-577-8743 office
(313)-577-6739 fax

 
 
 



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