[BioC] RMA background adjustment implementation in affy
Ben Bolstad
bmb at bmbolstad.com
Fri Jan 20 14:51:47 CET 2006
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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