[BioC] edgeR: Problem with subsetting a DGEList in latest package version

[Steve Lianoglou]

On Wed, Aug 13, 2014 at 2:58 PM, Steve Lianoglou
<lianoglou.steve at gene.com> wrote:
> Hi,
>
> On Wed, Aug 13, 2014 at 2:37 PM, Katja Hebestreit <katjah at stanford.edu> 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)

as well as:

R> length(out1)

-- 
Steve Lianoglou
Computational Biologist
Genentech