[BioC] RMA background adjustment implementation in affy

[Ben Bolstad]

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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