[R] cummeRbund MDSplot errors

[Bei Jun Chen]

Dear R mailing list members,


I was trying to make MDS plots using cummeRbund package on cuffdiff 
output files, but got some error messages instead.  I would really 
appreciate it if you could advise me on how to solve the problem.

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

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

With regards,

Bei Jun