[BioC] DESEQ problem

[Simon Anders]

Hi

On 09/19/2011 03:51 PM, Dawei Li wrote:
> Dear simon:
> I used your program to process the count data. I got the following
> message when I generate the plott:
>
>  > smoothScatter( log10(diagForIC$baseMean), log10(diagForIC$baseVar) )
[...]

> Error in if (!missing(bandwidth) && min(bandwidth) <= 0)
[..]

It is a bit hard to diagnose this without further information. Please 
try two things.

Have a look at 'head(diagForIC)'. Maybe something looks unusual there.

Then, try to plot without the kernel density estimation of smoothScatter:

plot( log10(diagForIC$baseMean), log10(diagForIC$baseVar), pch="." )

How does this look lie?

   Simon