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

[Katja Hebestreit]

Hi Mark,

Awesome! 

Thanks so much!!
- Katja

----- Original Message -----
From: "Mark Robinson" <mark.robinson at imls.uzh.ch>
To: "Katja Hebestreit" <katjah at stanford.edu>
Cc: bioconductor at r-project.org
Sent: Thursday, August 14, 2014 11:00:55 AM
Subject: Re: edgeR: Problem with subsetting a DGEList in latest package version

Hi Katja,

Apologies for the slow response.

I can reproduce this, thanks for sharing.  Gordon or I will commit a fix shortly.

In the meantime, try:

rc <- readDGE(files, labels = labels)
rc <- DGEList(rc$counts)

Then, subletting should work.

Cheers, Mark


On 13.08.2014, at 23:37, 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 `$<-.data.frame`(`*tmp*`, "group", value = integer(0)) : 
>  replacement has 0 rows, data has 39
> 
> Subsetting on genes works:
>> test <- rc[1,]
> 
> But subsetting on samples does not:
>> test <- rc[,1]
> Error in `$<-.data.frame`(`*tmp*`, "group", value = integer(0)) : 
>  replacement has 0 rows, data has 1
> 
> 
> The code worked a couple of weeks ago. I guess that there is a bug in the latest edgeR version that is causing this? Interestingly, I cannot reproduce the error using the example data in the DGEList manual:
> 
> y <- matrix(rnbinom(10000,mu=5,size=2),ncol=4)
> d <- DGEList(counts=y, group=rep(1:2,each=2))
> 
> 
> I would be grateful for any help!
> 
> Cheers,
> Katja
> 
> 
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C                  
> [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915    
> [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915   
> [7] LC_PAPER=en_US.iso885915       LC_NAME=C                     
> [9] LC_ADDRESS=C                   LC_TELEPHONE=C                
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C           
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] edgeR_3.6.7  limma_3.20.8
> 
> loaded via a namespace (and not attached):
> [1] compiler_3.1.0 tools_3.1.0   
>