[BioC] present/absent on 2-color oligo arrays

[Naomi Altman]

I have been having an on-going discussion with a colleague about 
whether he can say that some genes are "absent" in some tissues based 
on two-color microarrays - most recently, Agilent arrays.  There are 
a number of reasons that he would like to do this which are a mix of 
biology and QC.

He wants to use some (arbitrary) normalized expression level, or 
unnormalized level above local background or a percentile of the 
whole array background or ...

Any suggestions for papers about this?  (We can both think of a dozen 
ways to do it, but without experiments to see if they are valid 
methods, or at least a paper to
cite, I am reluctant to put the statistical seal of approval on any of them.)

Thanks,  Naomi

p.s. In case anyone thinks that high-throughput sequencing is going 
to end this type of discussion, have a look at the interesting paper 
by 't Hoen comparing sequencing and microarray 
results. 
http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Retrieve&list_uids=18927111 


Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111