[BioC] RMA background adjustment implementation in affy

[Naomi Altman]

Affy users might want to check out some of the great talks and papers 
that Ben has posted on his webpage:

http://stat-www.berkeley.edu/users/bolstad

--Naomi

At 08:51 AM 1/20/2006, Ben Bolstad wrote:
>There is no particular discrepancy. Refering here to the document that
>you refer to: It turns out for practical values of the parameters for
>this data type, that the second term on the numerator is essentially 0
>and the second term on the denominator is essentially 1. Thus the
>implementation ignores these terms.
>
>Ben
>
>
>On Wed, 2006-01-18 at 11:31 +0200, Mikko Korpela wrote:
> > Hello!
> >
> > There are some differences in the way the RMA background adjustment
> > formula is presented in different documents, and the way it's implemented
> > in the affy package. I wonder what causes the differences, and whether I
> > should be worried about the RMA values produced by affy.
> >
> > The relevant part of the code, I think, is this (copy-paste from affy
> > 1.9.6, same as in many previous versions of affy, at least in affy-1.5.8):
> >
> > ---
> >
> > void bg_adjust(double *PM,double *MM, double *param, int rows, int cols,
> > int co$  int i;
> >   double a;
> >
> >   for (i=0; i < rows; i++){
> >     a = PM[column*rows + i] - param[1] - param[0]*param[2]*param[2];
> >     PM[column*rows + i] = a + param[2] * phi(a/param[2])/Phi(a/param[2]);
> >   }
> >
> > }
> >
> > ---
> >
> > where the array "param" is as described by the following comment (also
> > copy-paste):
> >
> >  ** note we will assume that param[0] is alpha, param[1] is mu, param[2]
> > is sigma
> >
> > The documents that do not agree with the above are builtinMethods.pdf
> > (documentation of the affy package) and
> > 
> http://stat-www.berkeley.edu/users/bolstad/stuff/AffyLowLevelWorkshop_Poster_20$
> >
> > In particular, some terms are missing from both the numerator and the
> > denominator of the division operation in the affy implementation. The
> > documents also do not agree with each other...
> >
> > Am I missing something simple here? I hope someone knows the right
> > formula for the background adjustment and the reason why the
> > implementation is different (it seems) from the documentation.
> >
> > Thanks,
> >
> > Mikko
> >
> > _______________________________________________
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> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>
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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