[BioC] HELP| Agilent Sureprint data , CGH analysis with limma and snapCGH

[Gabriel Wajnberg [guest]]

> HC8204T <- read.maimages(c("HC8204_US09423728_252192411868_S01_CGH_107_Sep09_2_1.txt", "HC8204_US09423728_252192411868_S01_CGH_107_Sep09_2_3.txt"), source="agilent",columns = list(G = "gMedianSignal", Gb = "gBGMedianSignal", R = "rMedianSignal",
+ Rb = "rBGMedianSignal"), annotation = c("Row", "Col","FeatureNum", "ControlType","ProbeName"))
> HC8204T$design <- c(1,-1)
> RGT <- backgroundCorrect(HC8204T, method="minimum", offset=1)
> MAT <- normalizeWithinArrays(RGT, method="loess")
> pros <- processCGH(MA)
Error in order(MA$genes$Chr, MA$genes$Position) : 
  argument 1 is not a vector

So why does this error happens? is this the right way to analyze this data???

thanks
Gabriel



 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.1 (2012-06-22)
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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 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] snapCGH_1.26.0 DNAcopy_1.30.0 limma_3.12.1  

loaded via a namespace (and not attached):
 [1] aCGH_1.34.0           affy_1.34.0           affyio_1.24.0        
 [4] annotate_1.34.1       AnnotationDbi_1.18.1  Biobase_2.16.0       
 [7] BiocGenerics_0.2.0    BiocInstaller_1.4.7   cluster_1.14.2       
[10] DBI_0.2-5             genefilter_1.38.0     GLAD_2.18.0          
[13] grid_2.15.1           IRanges_1.14.4        lattice_0.20-6       
[16] MASS_7.3-20           multtest_2.12.0       pixmap_0.4-11        
[19] preprocessCore_1.18.0 RColorBrewer_1.0-5    RSQLite_0.11.1       
[22] splines_2.15.1        stats4_2.15.1         strucchange_1.4-7    
[25] survival_2.36-14      tilingArray_1.34.0    tools_2.15.1         
[28] vsn_3.24.0            XML_3.9-4             xtable_1.7-0         
[31] zlibbioc_1.2.0       


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