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

[Aryee, Martin,Ph.D.]

Hi Andrew,

One of the things readCharm does is match up the two channel files (_532 and _635) for each sample. The input to readCharm is file-centric (i.e. two files per sample), and the output is sample-centric. When annotating samples it tries to keep as many columns of the sample description file (sampleKey) you give it as possible. A requirement for this is that the values in a given column must be identical for a given green channel file and its matching red channel file. The warning ("The following columns in sampleKey contain discrepant values between channels and are being removed") means that this is not the case. You could take a look in column 1 and see if there is a discrepancy for one or more samples. (If you don't care to keep the information in column 1 you can safely ignore the warning.)

Best,
Martin

Martin Aryee
Departments of Pathology
Massachusetts General Hospital & Harvard Medical School
149 13th Street, Room 6016
Charlestown, Massachusetts 02129
Telephone: 617-726-5695
Fax: 617-726-5684
Email: aryee.martin at mgh.harvard.edu


On Nov 2, 2012, at 7:00 AM, guest at bioconductor.org wrote:
> 
> 
> From: "Andrew Beggs [guest]" <guest at bioconductor.org>
> Subject: [BioC] CHARM - The following columns in sampleKey...
> Date: November 2, 2012 4:25:08 AM EDT
> To: bioconductor at r-project.org, a.beggs at bham.ac.uk
> Cc: charm Maintainer <pmurakam at jhsph.edu>
> 
> 
> 
> 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
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
> 
> 
> 



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