[BioC] edgeR: Problem with subsetting a DGEList in latest package version
Steve Lianoglou
lianoglou.steve at gene.com
Thu Aug 14 00:00:19 CEST 2014
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
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