[BioC] How to get the number of Stat pairs used in MAS5

[James W. MacDonald]

Hi Julie,

Julie Dickerson wrote:
>>Hi Julie,
>>
>>Julie Dickerson wrote:
>>
>>>I am trying to figure out how to get the information about the number
>>>of
>>>stat_pairs used in the MAS5 computations for each probe set. THis
>>>information does not appear to be in the exprsSet class. Is it an
>>>intermediate value from one of the normalization steps? Does anyone
>>>know
>>>how to pull out this information?
>>
>>What exactly is a stat_pair?
>>
> 
> 
> According to the Affy literature:
> Stat Pair: The number of probe pairs available for this probe set
> Stat Pairs Used: the number of probe pairs used to make a detection call
> for a probe set.
> 
> The first one can, of course, be found from the cdf file with a little
> work. It is that Stat Pairs Used that I cannot figure out how to get.

Well, you could do it, but it might take a bit of work. It appears to me 
from the C code

https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy/src/mas5calls.c

that the stat pairs used is determined solely by saturation of the MM 
probe(s) in a probeset. I think the 'stock' setting for saturation is 
46000, so you could do something like this:

abatch <- ReadAffy()
mms <- mm(abatch, LISTRUE = TRUE)
mm.counts <- t(sapply(mms, function(x) apply(x, 2, function(y) sum(y > 
46000))))

Then you will have a matrix with the stat pairs used for each Affy ID 
and each chip.

HTH,

Jim


> 
> 
> 


-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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