Kasper,
I hear you. It's not so easy to achieve (because the function issuing the
warning doesn't know which gene it is working on), but we'll have a think
about it.
Best
Gordon
On Fri, 22 Jul 2011, Kasper Daniel Hansen wrote:
On Fri, Jul 22, 2011 at 9:31 AM, Sean Ruddy <srudd...@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
______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}
_______________________________________________
Bioc-sig-sequencing mailing list
Bioc-sig-sequencing@r-project.org
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
