[BioC] exonmap problems with rma normalization

[Gomez Moruno, Antonio]

Hi,

I got several .CEL files to do RMA using exonmap library below:

library(exonmap)
library(xmapcore)
library(exon.pmcdf)

raw.data<-read.exon(covdesc="covdesc")

raw.data at cdfName<-"exon.pmcdf"# which CDF file defines the array by setting the name of the .cdf

#RMA normalization and generate probeset summaries

x.rma<-rma(raw.data)

The problem is that at this point i got an error message:

Attaching package: 'exon.pmcdf'

The following object(s) are masked from 'package:hugene10stv1cdf':

    i2xy, xy2i

Error in .local(object, ...) : subscript out of bounds

This is my session info 

sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] exon.pmcdf_1.1        hugene10stv1cdf_2.8.0 exonmap_1.0.07       
 [4] plier_1.22.0          RMySQL_0.7-5          DBI_0.2-5            
 [7] RColorBrewer_1.0-2    simpleaffy_2.28.0     gcrma_2.24.1         
[10] genefilter_1.34.0     affy_1.30.0           Biobase_2.12.1       

loaded via a namespace (and not attached):
 [1] affyio_1.20.0         annotate_1.30.0       AnnotationDbi_1.14.1 
 [4] Biostrings_2.20.0     IRanges_1.10.0        preprocessCore_1.14.0
 [7] RSQLite_0.9-4         splines_2.13.0        survival_2.36-8      
[10] tools_2.13.0          xtable_1.5-6    

this is my raw data 

AffyBatch object
size of arrays=1050x1050 features (21 kb)
cdf=exon.pmcdf (1411189 affyids)
number of samples=12
number of genes=1411189
annotation=hugene10stv1
notes=


and this is my covdesc file

	group
IG100120JMI046-3gst_01.CEL	a
IG100120JMI045-3gst_01.CEL	a
IG100120JMI044-3gst_01.CEL	a
IG100120JMI043-3gst_01.CEL	a
IG100120JMI042-3gst_01.CEL	a
IG100120JMI041-3gst_01.CEL	a
IG100120JMI040-3gst_01.CEL	b
IG100120JMI039-3gst_01.CEL	b
IG100120JMI038-3gst_01.CEL	b
IG100120JMI037-3gst_01.CEL	b	
IG100120JMI036-3gst_01.CEL	b
IG100120JMI035-3gst_01.CEL	b


Can You help me please???

Thanks in advance

PS: i tried t