Awesome! Thanks! Problem solved!


On Fri, Oct 25, 2013 at 12:48 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> Hi,
>
> On Fri, Oct 25, 2013 at 10:08 AM, Alicia R. Pérez-Porro
> <alicia.r.perezporro@gmail.com> wrote:
> > Dear Michael and DESeq2 users,
> >
> > I started using DESeq2 three weeks ago. Even I was having some normal
> > problems for a newby person my experience was really positive and I was
> and
> > I am detecting more DEG than with DESeq(1).
> >
> > However suddenly I am encountering a new problem that wasn't coming up
> > previously:
> >
> >> resSig <- res[ res$padj < .1, ]
> > Error in normalizeSingleBracketSubscript(i, x, byrow = TRUE, exact =
> FALSE)
> > :
> >   subscript contains NAs
>
> resSig is a DataFrame, right?
>
> Does changing your code to this do the trick:
>
> R> resSig <- subset(res, padj < 0.1)
>
> Using `subset` instead of `[ ... ]` handles the case when there are
> NA's in the column you are filtering against.
>
> Otherwise you could do:
>
> R> resSig <- res[!is.na(res$padj) & res$padj < 0.1, ]
>
> > For me this is pretty weird because I've been using the exactly same
> > RScript and datasets for the last 3 weeks and I wasn't having this error
> > before.
>
> Wierd, indeed ... perhaps you recently upgraded to the new bioc2.13
> universe?
>
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>

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