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

[Andrzej Oleś]

Hi Katja,

Steve asked you for the length of the 'out1' object rathen then 'rc';
can you please share the output of

length(out1)


Cheers,
Andrzej

On Thu, Aug 14, 2014 at 3:13 AM, Katja Hebestreit <katjah at stanford.edu> wrote:
> Sorry, this is the right output:
>
>  > lapply(rc, dim)
> $samples
> [1] 40  3
>
> $counts
> [1] 23429    40
>
>> length(rc)
> [1] 937160
>
> -Katja
>
> ----- Original Message -----
> From: "Katja Hebestreit" <katjah at stanford.edu>
> To: "Steve Lianoglou" <lianoglou.steve at gene.com>
> Cc: "bioconductor at r-project.org list" <bioconductor at r-project.org>
> Sent: Wednesday, August 13, 2014 6:10:59 PM
> Subject: Re: [BioC] edgeR: Problem with subsetting a DGEList in latest package version
>
> Hi Steve,
>
> Here the output:
>
>
>> lapply(rc, dim)
> $samples
> [1] 39  6
>
> $counts
> [1] 23429    39
>
>> length(rc)
> [1] 913731
>
>
> Thanks for helping!!
> Katja
>
>
> ----- Original Message -----
> From: "Steve Lianoglou" <lianoglou.steve at gene.com>
> To: "Katja Hebestreit" <katjah at stanford.edu>
> Cc: "bioconductor at r-project.org list" <bioconductor at r-project.org>
> Sent: Wednesday, August 13, 2014 3:00:19 PM
> Subject: Re: [BioC] edgeR: Problem with subsetting a DGEList in latest package version
>
> On Wed, Aug 13, 2014 at 2:58 PM, Steve Lianoglou
> <lianoglou.steve at gene.com> wrote:
>> Hi,
>>
>> On Wed, Aug 13, 2014 at 2:37 PM, Katja Hebestreit <katjah at stanford.edu> wrote:
>>> Hello edgeR maintainers,
>>>
>>> I just ran into an error with code that is several weeks old. I cannot subset my DEGList object anymore. I created it from the HTseq output:
>>>
>>>
>>>> files <- list.files("Gene_counts",
>>>                     recursive = FALSE, pattern = "counts",
>>>                     full.names=TRUE)
>>>
>>>> rc <- readDGE(files, labels = labels)
>>>> dim(rc)
>>> [1] 23429    40
>>>
>>>> out1 <- which(colnames(rc) == "PGE_old_E")
>>>> rc <- rc[,-out1]
>>> Error in `$<-.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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