[BioC] CHARM - The following columns in sampleKey...

[Andrew Beggs [guest]]

Hello

I've being trying to get charm to read in some Nimblegen array data that I had to convert from PAIR to XYS, also making an annotation file. 

All goes swimmingly, until I try to  use readCharm, although the data appears to load, I get the following error when using readCharm:

The following columns in sampleKey contain discrepant values between channels and are being removed: 1

It's not clear what this means, as I have looked at the two channel files (532 and 635) and the structure is essentially the same. Subsequent analyses fail, I assume because of missing data. 

If I look at my loaded dataset with rawData I get the following:

> rawData
TilingFeatureSet (storageMode: lockedEnvironment)
assayData: 389307 features, 39 samples 
  element names: channel1, channel2 
protocolData
  rowNames: N3 N9 ... E2 (39 total)
  varLabels: filenamesChannel1 filenamesChannel2 dates1 dates2
  varMetadata: labelDescription channel
phenoData
  rowNames: N3 N9 ... E2 (39 total)
  varLabels: sampleID tissue arrayUT arrayMD
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.2006.11.02.hg18.cpg.promo

Can anyone help?

 -- 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] pd.2006.11.02.hg18.cpg.promo_0.0.1 oligo_1.22.0                      
 [3] oligoClasses_1.20.0                RSQLite_0.11.2                    
 [5] DBI_0.2-5                          charm_2.4.0                       
 [7] genefilter_1.40.0                  RColorBrewer_1.0-5                
 [9] fields_6.7                         spam_0.29-2                       
[11] SQN_1.0.5                          nor1mix_1.1-3                     
[13] mclust_4.0                         Biobase_2.18.0                    
[15] BiocGenerics_0.4.0                

loaded via a namespace (and not attached):
 [1] affxparser_1.30.0     affyio_1.26.0         annotate_1.36.0      
 [4] AnnotationDbi_1.20.2  BiocInstaller_1.8.3   Biostrings_2.26.2    
 [7] bit_1.1-9             BSgenome_1.26.1       codetools_0.2-8      
[10] corpcor_1.6.4         ff_2.2-9              foreach_1.4.0        
[13] GenomicRanges_1.10.3  gtools_2.7.0          IRanges_1.16.3       
[16] iterators_1.0.6       limma_3.14.1          MASS_7.3-22          
[19] multtest_2.14.0       parallel_2.15.2       preprocessCore_1.20.0
[22] siggenes_1.32.0       splines_2.15.2        stats4_2.15.2        
[25] survival_2.36-14      sva_3.4.0             XML_3.95-0.1         
[28] xtable_1.7-0          zlibbioc_1.4.0

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