[BioC] DESeq2 new error coming up

[Steve Lianoglou]

Hi,

On Fri, Oct 25, 2013 at 10:08 AM, Alicia R. Pérez-Porro
<alicia.r.perezporro at 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