[BioC] gcRMA: problem compute.affinities.local on gngnf1musa
Julien.Roux at unil.ch
Wed May 14 17:26:28 CEST 2008
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:
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
What can be wrong?
Then I tried:
> ai <- compute.affinities(cdfName(data))
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.
R version 2.7.0 (2008-04-22)
attached base packages:
 splines tools stats graphics grDevices utils datasets
 methods base
other attached packages:
 gngnf1musaprobe_1.8.1 gngnf1musacdf_1.14.0 gcrma_2.12.0
 matchprobes_1.12.0 affy_1.18.0 preprocessCore_1.2.0
 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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