hi Amandine,

It's hard to say, you are free to stick with a version you have of course.
But if you are doing ongoing research with incoming datasets, I would
encourage staying up to date and re-running the software. Of the x.y.z
release numbers, the z releases are limited to avoiding errors and clearing
up the documentation. The majority of the version bumps from the 1.0
release were sent to individual users with errors regarding datasets which
could not be shared. As the software was released for the first time in
March, the first two months saw a lot of bug fixes.

As far as the y releases, these are new features which we believe are
really worth upgrading for, and the argument for these goes in the NEWS
file. It's not that version 1.0 was not "stable", but that there was room
for improved functionality. For instance, we added automatic independent
filtering, and the ability to use contrasts in version 1.2. But ultimately,
this is up to you. A good reason to upgrade on the y versions is that the
release version is maintained, so we can push bug fixes if they come up.

Mike


On Fri, Nov 15, 2013 at 5:11 AM, <amandine.fournier@chu-lyon.fr> wrote:

>
> Dear Michael, Simon, Wolfgang and others,
>
> I have noticed that new versions of your nice DESeq2 package are released
> pretty often, which is really great, because it really improves the results.
> But as a consequence, I wonder when I can "freeze" my analyses. I
> sometimes have the feeling that there always is a new version of the
> package and that I always have to rerun the analyses...
> The last version I used is 1.0.19. I wonder if this version is "stable"
> enough to stop there ? Or do you advise me to use the last one (v1.2.5) ?
> Furthermore do you plan to release major changes in the next months ?
>
> Many thanks in advance.
> Best regards,
> Amandine
>
> -----
> Amandine Fournier
> Lyon Neuroscience Research Center
> & Lyon Civil Hospital (France)
>
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