[BioC] CHARM: Affymetrix 1.0R tiling arrays import

[Andrew Beggs [guest]]

Does anyone have any idea how to get Affy 1.0R tiling array data into CHARM?

I can't see any mathematical reason why CHARM shouldn't be able to estimate percentage methylation from these files, I just can't get the data structure to set up correctly.

I have imported the CEL files in with oligo, and ctrlIdx can identify regions correctly. I just can't get it to estimate percent methylation

Andrew

 -- output of sessionInfo(): 

R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
 [1] charm_2.4.0                        genefilter_1.40.0                 
 [3] RColorBrewer_1.0-5                 fields_6.7                        
 [5] spam_0.29-2                        SQN_1.0.5                         
 [7] nor1mix_1.1-3                      mclust_4.0                        
 [9] BSgenome.Hsapiens.UCSC.hg18_1.3.19 BSgenome_1.26.1                   
[11] Biostrings_2.26.2                  GenomicRanges_1.10.6              
[13] IRanges_1.16.5                     pd.hs.prompr.v02_0.0.1            
[15] RSQLite_0.11.2                     DBI_0.2-5                         
[17] oligo_1.22.0                       Biobase_2.18.0                    
[19] oligoClasses_1.20.0                BiocGenerics_0.4.0                

loaded via a namespace (and not attached):
 [1] affxparser_1.30.2     affyio_1.26.0         annotate_1.36.0      
 [4] AnnotationDbi_1.20.3  BiocInstaller_1.8.3   bit_1.1-9            
 [7] codetools_0.2-8       corpcor_1.6.4         ff_2.2-10            
[10] foreach_1.4.0         gtools_2.7.0          iterators_1.0.6      
[13] limma_3.14.4          MASS_7.3-23           multtest_2.14.0      
[16] parallel_2.15.2       preprocessCore_1.20.0 siggenes_1.32.0      
[19] splines_2.15.2        stats4_2.15.2         survival_2.37-2      
[22] sva_3.4.0             XML_3.95-0.1          xtable_1.7-0         
[25] zlibbioc_1.4.0       
> 


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