Dear BioC developers,
This is just to announce the public availability of the new package 'piano'.
Piano performs gene set analysis using various statistical methods, from
different gene level statistics and a wide range of gene-set collections.
Furthermore, the Piano package contains functions f
hi Steve,
Thanks for pointing me to this bug. I have fixed this in version 1.0.9. So
now rlogTransformation should accept the given dds just like
varianceStabilizingTransformation.
To avoid making a copy of the dds but still re-estimate dispersions, one
can do:
design(dds) <- ~ 1
mcols(dds)$disp
Dear all,
Recently, there was a discussion about generics conventions and the
possibility of defining normalize in BiocGenerics. I believe that the
consensus was to implement the latter in Bioc 2.13:
[ ... ]
On 21 February 2013 20:16, Hervé Pagès wrote:
> If we agree on this, I'll add it to our
Hi Laurent,
On 04/22/2013 12:55 PM, Laurent Gatto wrote:
Dear all,
Recently, there was a discussion about generics conventions and the
possibility of defining normalize in BiocGenerics. I believe that the
consensus was to implement the latter in Bioc 2.13:
[ ... ]
On 21 February 2013 20:16, H
Hi developers,
Just a reminder that now that the BioC release is behind us, we are
at the beginning of a new devel cycle, and this is a good time for
making the "deprecated -> defunct -> removal" shift in your package,
and for identifying features that are candidates for deprecation.
It's recomm
On Mon, Apr 22, 2013 at 3:56 PM, Hervé Pagès wrote:
> Hi developers,
>
> Just a reminder that now that the BioC release is behind us, we are
> at the beginning of a new devel cycle, and this is a good time for
> making the "deprecated -> defunct -> removal" shift in your package,
> and for identif
