Hi Gordon,

In addition to Kasper's email, is it possible to pass arguments to
maximizeInterpolant, for example to increase the max iterations? It appears
you can send additional arguments to dispCoxReidInerpolateTagwise but not to
maximizeInterpolant.

Thanks,
Sean


On Fri, Jul 22, 2011 at 6:39 AM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> On Fri, Jul 22, 2011 at 9:31 AM, Sean Ruddy <sruddy17@gmail.com> wrote:
> > Hi Gordon,
> >
> > Thanks for the reply. That's good to know I shouldn't be worried about
> the
> > results, but then again I'm not really sure, as you say, if I should even
> go
> > down this road. Using the standard edgeR normalization would also be
> > meaningless in my case unfortunately. I have two data sets of counts each
> > belonging to different organisms. One data set runs smoothly and the
> other
> > has all these problems yet the experiments done on both were exactly the
> > same. Kind of puzzling and unfortunate but I will investigate more into
> what
> > you're saying about the offsets and see if I can't adjust my
> > strategy. Thanks for the insights!
>
> While I agree with Gordon that having warnings in a few genes are
> hardly problematic, it would perhaps make sense to make it easy for
> the user to identify exactly which genes (rows) have warnings
> associated with them,  Having been bitten by convergence problems in
> the past, I believe it is always prudent to check the data. Just a
> suggestion, and I apoligize if this is already (easily) possible.
>
> Kasper
>

	[[alternative HTML version deleted]]

