Re: gcRMA: problem compute.affinities.local on gngnf1musa

Hi Julien,

Julien Roux wrote:
> Hello list,
> 
> In *Schuster et al. 2007 (http://genomebiology.com/2007/8/6/R125) a 
> method is presented allowing to correct *MAS5 present/absent calls based 
> on gcRMA transformed PM threshold values.
> The R script is available in sup data at 
> http://genomebiology.com/content/supplementary/gb-2007-8-6-r125-s1.txt
> 
> When trying to run it on my data I am faced to an error:
>  > data
> AffyBatch object
> size of arrays=854x854 features (11 kb)
> cdf=gnGNF1Musa (36182 affyids)
> number of samples=16
> number of genes=36182
> annotation=gngnf1musa
> notes= >  ai <- compute.affinities.local(data, Array=NULL)
> Adjusting for optical effect................Done.
> Computing base-position profiles for probe affinitiesErreur dans 
> complementSeq(seqs, start = 13, stop = 13) :
> Character N does not code for a nucleic acid.
> 
> I tried with other platforms (e.g. mgu74av2) and this works.
> So I guess this is due to an error in the annotation package gngnf1musa.
> I installed this package (custom array affymetrix) made available by Cei 
> Abreu-Goodger 
> (http://article.gmane.org/gmane.science.biology.informatics.conductor/13659)