hi Steve,

Thanks. Can you send a minimal example of the error? I can provide an
alternate formula without error:

> dds <- makeExampleDESeqDataSet()
> design(dds) <- formula(~ condition)
> rld <- rlogTransformation(dds)

Mike


On Fri, Apr 19, 2013 at 9:55 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Greetings,
>
> I'm kicking tires on the new DESeq2 package -- very nicely done, btw,
> thanks!.
>
> I have a quick question about the use of the variance and rlog
> transformations.
>
> It seems that both functions prefer to receive a DESeqDataSet with a
> design set to formula(~ 1). I say "prefer" because while rlogTransformation
> will error-out when the incoming dds has a different formula, the
> varianceStablizingTransform walks through it.
>
> If this in fact is the case, would it make sense to simply ensure this to
> be true by specifically hammering the design() of the dds to be as such
> from within the function itself?
>
> Unless I am missing something (if so, feel free to point it out), it seems
> like it would make the end-user's life easier w/o sacrificing much
> (anything) as the user wouldn't be forced to make a copy of the dds to pass
> to the function before it is called (and perhaps firing off a warning()
> when the incoming dds need to be changed as such).
>
> Thanks again,
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Department of Bioinformatics and Computational Biology
> Genentech
>
>

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