[BioC] vennDiagram error: Error in toptable

[Gordon Smyth]

 > Date: Tue, 22 Mar 2005 22:57:27 -0800
 > From: Dennis Hazelett <hazelett at uoneuro.uoregon.edu>
 > Subject: [BioC] vennDiagram error: Error in toptable
 > To: bioconductor at stat.math.ethz.ch
 >
 > Hello bioconductors,
 > while trying to make a vennDiagram I got the following error:
 >
 >  > results <- decideTests(eb,
 > method="separate",adjust.method="fdr",p.value=0.05)
 >  > results
 > TestResults matrix
 >      PPK PRO PCD
 > [1,]   0   0  -1
 > [2,]  -1   1   0
 > [3,]   0   1   0
 > [4,]  -1   0  -1
 > [5,]  -1   0   0
 > 6139 more rows ...
 >  > vennDiagram(results,method="separate",include="both")
 > Error in toptable(fit = fit[c("coefficients", "stdev.unscaled")], coef =
 > coef,  :
 >         (list) object cannot be coerced to integer

Your email seems to be garbled.  Firstly, vennDiagram() doesn't have an 
argument 'method'.  Secondly, the error message seems to be from quite a 
different function call -- there is no way that a call to vennDiagram() can 
lead to a call to toptable and to the error message given. The call given 
in the error message itself looks quite strange, and is not something which 
appears anywhere in the limma package. You certainly don't seem to be using 
the commands correctly, or reporting correctly what has happened.

Gordon

 > Has anyone seen this before or know how to fix it? I think I passed the
 > right arguments (?) based on the help files. I'm using R 2.0.1 and
 > Bioconductor release 1.5.
 > Thanks
 > -Dennis