Re: edgeR: Problem with subsetting a DGEList in latest package version

Steve Lianoglou <lianoglou.steve-RuTDbSqP/[email protected]> Wed, 13 Aug 2014 14:58:48 -0700

Newsgroups	gmane.science.biology.informatics.conductor
Message-ID	<CAHA9McNyHmOyRU_Gno1cDxK_6+nsOQ_khQ+nAzbGwnukqaGjLA@mail.gmail.com>

Hi,

On Wed, Aug 13, 2014 at 2:37 PM, Katja Hebestreit <katjah-FGKo4X94FMn2fBVCVOL8/[email protected]> wrote:
> Hello edgeR maintainers,
>
> I just ran into an error with code that is several weeks old. I cannot subset my DEGList object anymore. I created it from the HTseq output:
>
>
>> files <- list.files("Gene_counts",
>                     recursive = FALSE, pattern = "counts",
>                     full.names=TRUE)
>
>> rc <- readDGE(files, labels = labels)
>> dim(rc)
> [1] 23429    40
>
>> out1 <- which(colnames(rc) == "PGE_old_E")
>> rc <- rc[,-out1]
> Error in `$<-.data.frame`(`*tmp*`, "group", value = integer(0)) :
>   replacement has 0 rows, data has 39

Can please you show us the output of:

R> lapply(rc, dim)

Thanks,
-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech

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