edgeR: Problem with subsetting a DGEList in latest package version

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Katja Hebestreit ▴ 130

@katja-hebestreit-6495

Last seen 4.4 years ago

United States

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

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ADD COMMENT • link updated 10.3 years ago by Mark Robinson ▴ 880 • written 10.3 years ago by Katja Hebestreit ▴ 130

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Mark Robinson ▴ 880

@mark-robinson-4908

Last seen 6.1 years ago

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 >

ADD COMMENT • link 10.3 years ago Mark Robinson ▴ 880

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Hi Mark, Awesome! Thanks so much!! - Katja ----- Original Message ----- From: "Mark Robinson" <mark.robinson@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 >

ADD REPLY • link 10.3 years ago Katja Hebestreit ▴ 130

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 21 months ago

United States

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) Thanks, -steve -- Steve Lianoglou Computational Biologist Genentech

ADD COMMENT • link 10.3 years ago Steve Lianoglou ★ 13k

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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

ADD REPLY • link 10.3 years ago Steve Lianoglou ★ 13k

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

ADD REPLY • link 10.3 years ago Katja Hebestreit ▴ 130

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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@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 $counts [1] 23429 39 > length(rc) [1] 913731 Thanks for helping!! Katja ----- Original Message ----- From: "Steve Lianoglou" <lianoglou.steve@gene.com> To: "Katja Hebestreit" <katjah at="" stanford.edu=""> Cc: "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> Sent: Wednesday, August 13, 2014 3:00:19 PM Subject: Re: [BioC] edgeR: Problem with subsetting a DGEList in latest package version On Wed, Aug 13, 2014 at 2:58 PM, Steve Lianoglou <lianoglou.steve at="" gene.com=""> wrote: > Hi, > > On Wed, Aug 13, 2014 at 2:37 PM, Katja Hebestreit <katjah at="" stanford.edu=""> wrote: >> Hello edgeR maintainers, >> >> I just ran into an error with code that is several weeks old. I cannot subset my DEGList object anymore. I created it from the HTseq output: >> >> >>> files <- list.files("Gene_counts", >> recursive = FALSE, pattern = "counts", >> full.names=TRUE) >> >>> rc <- readDGE(files, labels = labels) >>> dim(rc) >> [1] 23429 40 >> >>> out1 <- which(colnames(rc) == "PGE_old_E") >>> rc <- rc[,-out1] >> Error in `$<-.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 _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 10.3 years ago Katja Hebestreit ▴ 130

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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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 10.3 years ago Andrzej Oleś ▴ 750

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Hi Andrzej, > length(out1) [1] 1 Also, this does not work: > test <- rc[,1] Error in `$<-.data.frame`(`*tmp*`, "group", value = integer(0)) : replacement has 0 rows, data has 1 Thanks for helping! Katja ----- Original Message ----- From: "Andrzej Ole?" <andrzej.oles@gmail.com> To: "Katja Hebestreit" <katjah at="" stanford.edu=""> Cc: "Steve Lianoglou" <lianoglou.steve at="" gene.com="">, "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> Sent: Thursday, August 14, 2014 1:50:20 AM Subject: Re: [BioC] edgeR: Problem with subsetting a DGEList in latest package version 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 10.3 years ago Katja Hebestreit ▴ 130

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