[BioC] gcrma on affy xlaevis arrays

[Tobias Straub]

Hi
I am facing the following problem calling gcrma on an affy X. laevis array. is there a quick solution or do i have to dig deep?
tia t.

> a
AffyBatch object
size of arrays=984x984 features (20 kb)
cdf=X_laevis_2 (32635 affyids)
number of samples=8
number of genes=32635
annotation=xlaevis2
notes=
> gcrma(a)
Adjusting for optical effect........Done.
Computing affinities.Done.
Error in sample(1:length(as.matrix(pms)[index.affinities, ]), 25000) : 
  cannot take a sample larger than the population when 'replace = FALSE'
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] xlaevis2probe_2.8.0       xlaevis2cdf_2.8.0         arrayQualityMetrics_3.8.0
 [4] geneplotter_1.30.0        lattice_0.19-23           annotate_1.30.0          
 [7] simpleaffy_2.28.0         gcrma_2.24.1              genefilter_1.34.0        
[10] annaffy_1.24.0            KEGG.db_2.5.0             GO.db_2.5.0              
[13] affy_1.30.0               xlaevis.db_2.5.0          org.Xl.eg.db_2.5.0       
[16] RSQLite_0.9-4             DBI_0.2-5                 AnnotationDbi_1.14.1     
[19] Biobase_2.12.1           

loaded via a namespace (and not attached):
 [1] affyio_1.20.0         affyPLM_1.28.5        beadarray_2.2.0       Biostrings_2.20.0   
 [5] Cairo_1.4-9           cluster_1.13.3        grid_2.13.0           Hmisc_3.8-3         
 [9] hwriter_1.3           IRanges_1.10.0        latticeExtra_0.6-14   limma_3.8.1         
[13] preprocessCore_1.14.0 RColorBrewer_1.0-2    setRNG_2009.11-1      splines_2.13.0       
[17] survival_2.36-5       SVGAnnotation_0.9-0   tools_2.13.0          vsn_3.20.0           
[21] XML_3.2-0             xtable_1.5-6         


----------------------------------------------------------------------
Dr. Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, München D