[BioC] rma for tiling arrays (oligo package)

[Steve Lianoglou]

Hi,

I have a question that's slightly off-topic, but I don't think it's  
enough to change the subject.

I wanted to give a shot at using the rma.background.correction on the  
drosophila tiling array that I'm working with. As a disclaimer, I  
haven't been using all of the BioC tools to their fullest and have  
been doing some stuff on my own.

My question is related to the following ..

James wrote:

>>> I would personally just copy the functions normalize.quantiles()  
>>> and rma.background.correct() from affy into a file (say,  
>>> affysources.R) and then source that into R. Both of these  
>>> functions want you to pass a matrix, so you would want to extract  
>>> the pm data from your AllArrays object, run  
>>> rma.background.correct() and then normalize.quantiles() on the  
>>> matrix, and then put that back into AllArrays.


You seem to suggest that the rma.background.correction works on only  
the perfect match (PM) probes. I wanted to try to extract these probes  
from my data. In doing so, something is mystifying me.

I've reblasted the probes on my array to the latest drosophila genome  
so that I could have better annotation for my data and interpretation.  
If I consider only probes on the array with >= 1 perfect match to the  
genome:

   * Some of the probes affy annotates as PM don't have any such  
perfect match; and
   * Some of the probes affy annotates as MM *do* have >= 1 perfect  
match.

Is this expected?

Assuming my code that reblasts, parses the results and anottates my  
probes is bug free, (I'll admit  this is a possibility, but I think  
I've tested it well enough) what does it mean for a PM probe not to  
have any hit to the genome, and MM probes to have some? I expected  
this not to be the case, but I'm not understanding with the whole use  
of PM/MM probes.

Should I just consider any probe that has >= 1 perfect alignment to  
the genome as a PM? For what it's worth, I'm not planning on using the  
MM probes in my signal normalization technique.

Thanks for any help,
-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Cornell Medical College

http://cbio.mskcc.org/~lianos