[BioC] Ideal Mismatch value

[James W. MacDonald]

Wang, Yonghong (NIH/NCI) [C] wrote:
> Hi, All:
> As part of the suggestions from a reviewer of my submitted paper, I am
> asked to provide the IM (Ideal Mismatch) values generated from MAS5 for
> some probes of some probeset. I know BioConductor can provide both PM
> and MM intensities for each individual probes, would someone please tell
> me whether I can also get IM values (when applicable) from cel file by
> using BioConductor? If we can, how?

The short answer is no.

The long answer is yes, but it would take some work to do so. The work 
is done by the function pmcorrect.mas(), which is called on each 
probeset individually. You would have to background correct your 
AffyBatch using bgcorrect.mas(), then for whichever probesets you are 
interested in, you could either create your own function based on 
pmcorrect.mas() that returns the IM values, and just run that function 
on the probeset in question. Or you could just debug() the existing 
pmcorrect.mas(), and when the IM values you are interested in appear, 
you could dump them into the .GlobalEnv using the <<- operator.

Note that pmcorrect.mas() takes a ProbeSet object as input. What is done 
in expresso() is to make an empty ProbeSet object, then get the PM and 
MM values for a particular probeset (using a combination of get() and 
intensity(), although you could probably just use pm(abatch, 
"probesetID")) and then stick these values in the pm and mm slots of the 
ProbeSet. This is done in computeExprSet().

If it sounds like a lot of work, it is. If you really need these data, 
you should look at the functions pmcorrect.mas(), and computeExprSet() 
to see how it is done and to figure out how to do it yourself.

To see the functions you can either download the sources from BioC and 
grep them out of the R directory (preferable), or you can just load the 
affy package and type

pmcorrect.mas

and

showMethods(computeExprSet, class = "AffyBatch", includeDefs = TRUE)

Best,

Jim


> 
> Thanks a lot for your help.
> 
> Best regards
> 
> YH Wang
> 
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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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