[BioC] "normalize.quantiles.robust" produces the SAME intensities from different weights?!

[Ben Bolstad]

Thanks for this report. It turned out that there was a minor bug in
normalize.quantiles.robust() and incorrect parameters were being passed
down to the C code. This is due to some changes I made many months ago
now.

A corrected version of the function will appear in the next version of
affy. But briefly the final line in that function should have been:


 .Call("R_qnorm_robust_c",x,copy,weights,as.integer(use.median),as.integer(use.log2),as.integer(use.huber),PACKAGE="affy")

Best,

Ben

On Wed, 2006-09-20 at 17:29 +0200, k. brand wrote:
> Dear BioCers,
> 
> My interpretation of the function "normalize.quantiles.robust" is the 
> ability to selectively increase or reduce the contribution of specific 
> chips during normalization.
> 
> Although i get different results from equally weighted chips (which is 
> the same as "justRMA" as a verification), all variations of unequal 
> weightings produce do the SAME intensities?! See 2 examples below.
> 
> Can some one find the error in my script, or better yet, give an example 
>   of a better way to achieve my objective-
> 
> to selectively 'pull' low intensities of duplicate chips form a poor hyb 
> (on expired arrays), up to the levels of duplicate chips of a good 
> hyb(on unexpired arrays).
> 
> TIA,
> 
> Karl
> 
>