[BioC] Query regarding SomatiSignature bioconductor package

[Anand [guest]]

Hi all,

I have been using SomaticSignature BC package to predict signatures. I am following the examples provided in vignette. However I have some doubts.

1.I have data from a single study (AML) with mutations obtained from 14 patients. In this case, how do I group the data ? If I group the data by ‘study’ as in vignette, I am getting an error while running nmfSignatures function.(I guess it’s because the dimension of matrix
(sca_occurance) has only one column corresponding to the single study performed ) Can I group it based on patients (sampleNames) instead ?

2.How do I choose the number R (number of signatures to obtain) ? I guess it should be less than number of columns of sca_occurances ? In a recent publication (Nicocolo Bolli et al , 2013, nat. com)  involving single study (multiple myeloma with 52 patients), they mention - the have found two signatures, does it mean they have set the number of signatures (R argument in nmfSignatures()) to 2?

My apologies if the question is not in the proper format. 

Thank you,

-Anand.


 -- output of sessionInfo(): 

R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_Singapore.1252  LC_CTYPE=English_Singapore.1252   
[3] LC_MONETARY=English_Singapore.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Singapore.1252    

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

other attached packages:
 [1] fastICA_1.2-0                  stringr_0.6.2                 
 [3] exomeCopy_1.10.0               SomaticCancerAlterations_1.0.0
 [5] SomaticSignatures_1.0.1        Biobase_2.24.0                
 [7] ggbio_1.12.4                   ggplot2_1.0.0                 
 [9] reshape2_1.4                   VariantAnnotation_1.10.1      
[11] Rsamtools_1.16.0               Biostrings_2.32.0             
[13] XVector_0.4.0                  GenomicRanges_1.16.3          
[15] GenomeInfoDb_1.0.2             IRanges_1.22.8                
[17] BiocGenerics_0.10.0           

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.26.0    BatchJobs_1.2           BBmisc_1.6             
 [4] BiocParallel_0.6.1      biomaRt_2.20.0          biovizBase_1.12.1      
 [7] bitops_1.0-6            brew_1.0-6              BSgenome_1.32.0        
[10] cluster_1.15.2          codetools_0.2-8         colorspace_1.2-4       
[13] DBI_0.2-7               dichromat_2.0-0         digest_0.6.4           
[16] doParallel_1.0.8        fail_1.2                foreach_1.4.2          
[19] Formula_1.1-1           GenomicAlignments_1.0.1 GenomicFeatures_1.16.2 
[22] grid_3.1.0              gridBase_0.4-7          gridExtra_0.9.1        
[25] gtable_0.1.2            gtools_3.4.1            Hmisc_3.14-4           
[28] iterators_1.0.7         labeling_0.2            lattice_0.20-29        
[31] latticeExtra_0.6-26     MASS_7.3-31             munsell_0.4.2          
[34] NMF_0.20.5              pcaMethods_1.54.0       pkgmaker_0.22          
[37] plyr_1.8.1              proto_0.3-10            RColorBrewer_1.0-5     
[40] Rcpp_0.11.2             RCurl_1.95-4.1          registry_0.2           
[43] rngtools_1.2.4          RSQLite_0.11.4          rtracklayer_1.24.2     
[46] scales_0.2.4            sendmailR_1.1-2         splines_3.1.0          
[49] stats4_3.1.0            survival_2.37-7         tools_3.1.0            
[52] XML_3.98-1.1            xtable_1.7-3            zlibbioc_1.10.0

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