[BioC] gcRMA: problem compute.affinities.local on gngnf1musa

Julien Roux Julien.Roux at unil.ch
Wed May 14 17:26:28 CEST 2008

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 

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
 >  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 
at ftp://ftp.sanger.ac.uk/pub/cei/gngnf1_R_packages.tar.gz
What can be wrong?

Then I tried:
 > ai <- compute.affinities(cdfName(data))
Computing affinities.Done.

This worked. However I am not sure it is doing the same thing (Adjusting 
for optical effect? Computing base-position profiles for probe affinities?)
What is the difference between compute.affinities and 

Thanks for your help to clarify this.

 > sessionInfo()
R version 2.7.0 (2008-04-22)


attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base    

other attached packages:
[1] gngnf1musaprobe_1.8.1 gngnf1musacdf_1.14.0  gcrma_2.12.0        
[4] matchprobes_1.12.0    affy_1.18.0           preprocessCore_1.2.0
[7] affyio_1.8.0          Biobase_2.0.1       

Julien Roux, PhD student
Department of Ecology and Evolution
Biophore, University of Lausanne, 1015 Lausanne, Switzerland
tel: +41 21 692 4221    fax: +41 21 692 4165

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