R help - Dec 2015 - cummeRbund MDSplot errors

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

This is a Bioconductor package. So I think you would do better to post
on the Bioconductor list, not here.


Cheers,
Bert
Bert Gunter

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
   -- Clifford Stoll


On Tue, Dec 1, 2015 at 6:27 AM, Bei Jun Chen <b.j.chen at unsw.edu.au>
wrote:
> 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
>
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