Dear Community,

I was trying to make MDS plots using cummeRbund package on cuffdiff output files, but got some error messages instead. 

I am running Ubuntu 15.10, R version 3.2.2, cummeRbund version 2.13.  My code and error messages are as follows:

> library("cummeRbund")
> cuff <- readCufflinks()
> MDS <- MDSplot(genes(cuff))
Error in cmdscale(d, eig = TRUE, k = 2) :
  'k' must be in {1, 2, ..  n - 1}
> MDS <- MDSplot(genes(cuff), replicates=T)
Error in sqliteSendQuery(con, statement, bind.data) :
  error in statement: near "from": syntax error

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.10

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

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] cummeRbund_2.12.0    Gviz_1.14.0          rtracklayer_1.30.1  
 [4] GenomicRanges_1.22.1 GenomeInfoDb_1.6.1   IRanges_2.4.4       
 [7] S4Vectors_0.8.3      fastcluster_1.1.16   reshape2_1.4.1      
[10] ggplot2_1.0.1        RSQLite_1.0.0        DBI_0.3.1           
[13] BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.0.1 VariantAnnotation_1.16.3  
 [3] splines_3.2.2              lattice_0.20-33           
 [5] colorspace_1.2-6           htmltools_0.2.6           
 [7] yaml_2.1.13                GenomicFeatures_1.22.5    
 [9] XML_3.98-1.3               survival_2.38-3           
[11] foreign_0.8-66             BiocParallel_1.4.0        
[13] RColorBrewer_1.1-2         lambda.r_1.1.7            
[15] matrixStats_0.15.0         plyr_1.8.3                
[17] stringr_1.0.0              zlibbioc_1.16.0           
[19] Biostrings_2.38.2          munsell_0.4.2             
[21] gtable_0.1.2               futile.logger_1.4.1       
[23] knitr_1.11                 latticeExtra_0.6-26       
[25] Biobase_2.30.0             biomaRt_2.26.1            
[27] AnnotationDbi_1.32.0       proto_0.3-10              
[29] Rcpp_0.12.2                acepack_1.3-3.3           
[31] BSgenome_1.38.0            scales_0.3.0              
[33] Hmisc_3.17-0               XVector_0.10.0            
[35] Rsamtools_1.22.0           gridExtra_2.0.0           
[37] digest_0.6.8               stringi_1.0-1             
[39] biovizBase_1.18.0          tools_3.2.2               
[41] bitops_1.0-6               magrittr_1.5              
[43] RCurl_1.95-4.7             dichromat_2.0-0           
[45] Formula_1.2-1              cluster_2.0.3             
[47] futile.options_1.0.0       MASS_7.3-45               
[49] rmarkdown_0.8.1            rpart_4.1-10              
[51] GenomicAlignments_1.6.1    nnet_7.3-11           

I've checked the cummeRbund manual and couldn't find clues on how to fix the problem.  I'd appreciate it if anyone knows how to solve it.  Thank you in advance.

Bei Jun

Hi Bei,

Can you please let me know what version of cufflinks you are using?  Is it greater than v2.1?

Also, can you try to rebuild your cummeRbund database using

cuff<-readCufflinks(rebuild=T)

And see if that makes a difference?  My concern is that your cummeRbund database was not build correctly the first time through.  Do you have any other problems with other parts of cummeRbund or just MDS?

-Loyal