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

[k. brand]

Ben, thank you for the fast help- it worked!

Karl

on 9/21/2006 5:16 AM Ben Bolstad said the following:
> 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
>>
>>
> 
> 

-- 
Karl Brand <k.brand at erasmusmc.nl>
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
lab +31 (0)10 408 7409 fax +31 (0)10 408 9468