
Dear,

Starting to analyse exon arrays from Affymetrix, I used  exonmap to read in the raw data . I would like to get a view on the raw data before furhter downstream analysis. One of the things I had in mind to do is a boxplot and an MAplot on the raw data. Is that possible?

What I tried is the following:

	dataRaw <- read.exon(covdesc = "samplesImportFormat.txt")
dataRaw@cdfName <- "exon.pmcdf"
boxplot(dataRaw)
MAplot(dataRaw)

	

The boxplot looks fine but I get a warning:
"some row.names duplicated: 4,6,7,8,9,10,11,17,..."
Although all rownames(exprs(dataRaw)) are unique as well as all colnames(exprs(dataRaw)). Is it possible to avoid this warning?

The MAplot does not produce a graph and generates an error:
"Error in quantile.default(as.numeric(x), c(0.25, 0.75), na.rm = na.rm, : 
missing values and NaN's not allowed if 'na.rm' is FALSE"
Although there seems  to be no NA's in my data:
summary(exprs(dataRaw))
    6039.CEL          6040.CEL       
 Min.   :   32.0   Min.   :   32.00  
 1st Qu.:   53.0   1st Qu.:   52.00  
 Median :   58.0   Median :   58.00  
 Mean   :  105.9   Mean   :   95.08  
 3rd Qu.:   71.0   3rd Qu.:   70.00  
 Max.   :65534.0   Max.   :65534.00  


Is there something that I have overlooked which is the basis for these issues?

Thanks in advance for your help!

Best regards,

An


PS: sessionInfo()

R version 2.6.2 (2008-02-08) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
 [1] gplots_2.3.2         gdata_2.4.0          gtools_2.4.0        
 [4] geneplotter_1.16.0   lattice_0.17-6       annotate_1.16.1     
 [7] xtable_1.5-2         AnnotationDbi_1.0.6  RSQLite_0.6-7       
[10] exon.pmcdf_1.1       exonmap_1.4.3        plier_1.8.0         
[13] RColorBrewer_1.0-2   simpleaffy_2.14.05   gcrma_2.10.0        
[16] matchprobes_1.10.0   genefilter_1.16.0    survival_2.34       
[19] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1        
[22] Biobase_1.16.3       RMySQL_0.6-0         DBI_0.2-4           

loaded via a namespace (and not attached):
[1] grid_2.6.2         KernSmooth_2.22-22 rcompgen_0.1-17   



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