Question: DESeq2 design formula error?
0
5.8 years ago by
United States
Charles Determan Jr140 wrote:
Greetings, I am trying to run an interaction formula with DESeq2. I try and run the following code and get the following error: > design(DESeq.cds) <- formula(~ subject+group+group:times)> DESeq.cds <- DESeq(DESeq.cds)estimating size factorsestimating dispersionsyou had estimated dispersions, replacing thesegene-wise dispersion estimatesError in modelMatrixNames[match(convertNames$from, modelMatrixNames)] <- convertNames$to : NAs are not allowed in subscripted assignments I am not sure exactly what this means. I have uneven groups sizes but it doesn't seem to be an issue when I have the design: > design(DESeq.cds) <- formula(~ subject+times+group+group:times) But the above formula doesn't provide the contrasts I would like. I would like to have the coefficients to be as follows so I can report how the genes change in response in the different groups over time. [1] "(Intercept)" "subject.2" [3] "subject.3" "subject.4" [5] "subject.5" "group.Treated" [7] "group.Control:times1 "group.Treated:times1" [9] "group.Control:times2 "group.Treated:times2" [11] "group.Control:times3 "group.Treated:times3" Thanks for any insight, -- Charles Determan Integrated Biosciences PhD Candidate University of Minnesota [[alternative HTML version deleted]]
deseq deseq2 • 631 views
modified 5.8 years ago by Steve Lianoglou12k • written 5.8 years ago by Charles Determan Jr140
0
5.8 years ago by
Denali
Steve Lianoglou12k wrote:
Hi Charles, On Mon, Jul 15, 2013 at 12:23 PM, Charles Determan Jr <deter088 at="" umn.edu=""> wrote: > Greetings, > > I am trying to run an interaction formula with DESeq2. I try and run the > following code and get the following error: > >> design(DESeq.cds) <- formula(~ subject+group+group:times)> DESeq.cds <- DESeq(DESeq.cds)estimating size factorsestimating dispersionsyou had estimated dispersions, replacing thesegene-wise dispersion estimatesError in modelMatrixNames[match(convertNames$from, modelMatrixNames)] <- convertNames$to : > NAs are not allowed in subscripted assignments > > > I am not sure exactly what this means. I have uneven groups sizes but it > doesn't seem to be an issue when I have the design: > >> design(DESeq.cds) <- formula(~ subject+times+group+group:times) > > > But the above formula doesn't provide the contrasts I would like. I would > like to have the coefficients to be as follows so I can report how the > genes change in response in the different groups over time. This is related to my recent posting over @ bioc-devel which Mike just committed a fix for: https://stat.ethz.ch/pipermail/bioc-devel/2013-July/004463.html The good news is that Mike has patched the current and devel versions, so you should be able to get them soon once version 1.0.18 propagates through the build system: https://stat.ethz.ch/pipermail/bioc-devel/2013-July/004503.html Or, optionally, you can d/l from SVN and compile/install yourself, if you are equipped to do so. HTH, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
Thank you Steve and to Mike as well for the patch. Do you (or anyone) if there is a rough timeline as to when the patched package will be made available? I am on a restricted timeline and I have not compiled and installed an R package before but I will certainly give it a try if the patched package won't be out soon. Thanks again, Charles On Mon, Jul 15, 2013 at 3:45 PM, Steve Lianoglou <lianoglou.steve@gene.com>wrote: > Hi Charles, > > > On Mon, Jul 15, 2013 at 12:23 PM, Charles Determan Jr <deter088@umn.edu> > wrote: > > Greetings, > > > > I am trying to run an interaction formula with DESeq2. I try and run the > > following code and get the following error: > > > >> design(DESeq.cds) <- formula(~ subject+group+group:times)> DESeq.cds <- > DESeq(DESeq.cds)estimating size factorsestimating dispersionsyou had > estimated dispersions, replacing thesegene-wise dispersion estimatesError > in modelMatrixNames[match(convertNames$from, modelMatrixNames)] <- > convertNames$to : > > NAs are not allowed in subscripted assignments > > > > > > I am not sure exactly what this means. I have uneven groups sizes but it > > doesn't seem to be an issue when I have the design: > > > >> design(DESeq.cds) <- formula(~ subject+times+group+group:times) > > > > > > But the above formula doesn't provide the contrasts I would like. I > would > > like to have the coefficients to be as follows so I can report how the > > genes change in response in the different groups over time. > > This is related to my recent posting over @ bioc-devel which Mike just > committed a fix for: > > https://stat.ethz.ch/pipermail/bioc-devel/2013-July/004463.html > > The good news is that Mike has patched the current and devel versions, > so you should be able to get them soon once version 1.0.18 propagates > through the build system: > > https://stat.ethz.ch/pipermail/bioc-devel/2013-July/004503.html > > Or, optionally, you can d/l from SVN and compile/install yourself, if > you are equipped to do so. > > HTH, > -steve > > -- > Steve Lianoglou > Computational Biologist > Bioinformatics and Computational Biology > Genentech > -- Charles Determan Integrated Biosciences PhD Candidate University of Minnesota [[alternative HTML version deleted]]
Hi Charles, On Tuesday, July 16, 2013, Charles Determan Jr wrote: > Thank you Steve and to Mike as well for the patch. Do you (or anyone) if > there is a rough timeline as to when the patched package will be made > available? I am on a restricted timeline and I have not compiled and > installed an R package before but I will certainly give it a try if the > patched package won't be out soon. I'm actually surprised that it hasn't propagated over to the servers yet ... perhaps it will be there later today (noon-ish PST) or tomorrow Compiling and installing yourself is as easy as running "R CMD INSTALL package_name" (depending on the os you are on) so I'd definitely recommend you try that. You need to ensure you have a valid build tool gain on your machine that includes gcc. If you are running osx or Linux, setting up a sane build environment is quite easy. From what I understand, it is also relatively easier to set this up on windows with newer versions of r (you should be on 3.0.x anyway) ... So, I think you can give it a shot to see? -Steve > Thanks again, > Charles > > > On Mon, Jul 15, 2013 at 3:45 PM, Steve Lianoglou > <lianoglou.steve@gene.com <javascript:;="">>wrote: > > > Hi Charles, > > > > > > On Mon, Jul 15, 2013 at 12:23 PM, Charles Determan Jr <deter088@umn.edu<javascript:;> > > > > wrote: > > > Greetings, > > > > > > I am trying to run an interaction formula with DESeq2. I try and run > the > > > following code and get the following error: > > > > > >> design(DESeq.cds) <- formula(~ subject+group+group:times)> DESeq.cds > <- > > DESeq(DESeq.cds)estimating size factorsestimating dispersionsyou had > > estimated dispersions, replacing thesegene-wise dispersion estimatesError > > in modelMatrixNames[match(convertNames$from, modelMatrixNames)] <- > > convertNames$to : > > > NAs are not allowed in subscripted assignments > > > > > > > > > I am not sure exactly what this means. I have uneven groups sizes but > it > > > doesn't seem to be an issue when I have the design: > > > > > >> design(DESeq.cds) <- formula(~ subject+times+group+group:times) > > > > > > > > > But the above formula doesn't provide the contrasts I would like. I > > would > > > like to have the coefficients to be as follows so I can report how the > > > genes change in response in the different groups over time. > > > > This is related to my recent posting over @ bioc-devel which Mike just > > committed a fix for: > > > > https://stat.ethz.ch/pipermail/bioc-devel/2013-July/004463.html > > > > The good news is that Mike has patched the current and devel versions, > > so you should be able to get them soon once version 1.0.18 propagates > > through the build system: > > > > https://stat.ethz.ch/pipermail/bioc-devel/2013-July/004503.html > > > > Or, optionally, you can d/l from SVN and compile/install yourself, if > > you are equipped to do so. > > > > HTH, > > -steve > > > > -- > > Steve Lianoglou > > Computational Biologist > > Bioinformatics and Computational Biology > > Genentech > > > > > > -- > Charles Determan > Integrated Biosciences PhD Candidate > University of Minnesota > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <javascript:;> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech [[alternative HTML version deleted]]
Hi all, it has, this morning. I have installed other package and it has asked me to updated it. J > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: *[1] DESeq2_1.0.18 * RcppArmadillo_0.3.900.0 Rcpp_0.10.4 [4] lattice_0.20-15 Biobase_2.20.1 GenomicRanges_1.12.4 [7] IRanges_1.18.2 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.22.6 DBI_0.2-7 RColorBrewer_1.0-5 [4] RSQLite_0.11.4 XML_3.95-0.2 annotate_1.38.0 [7] genefilter_1.42.0 grid_3.0.1 locfit_1.5-9.1 [10] splines_3.0.1 stats4_3.0.1 survival_2.37-4 [13] tools_3.0.1 xtable_1.7-1 2013/7/16 Steve Lianoglou <lianoglou.steve@gene.com> > Hi Charles, > > On Tuesday, July 16, 2013, Charles Determan Jr wrote: > > > Thank you Steve and to Mike as well for the patch. Do you (or anyone) if > > there is a rough timeline as to when the patched package will be made > > available? I am on a restricted timeline and I have not compiled and > > installed an R package before but I will certainly give it a try if the > > patched package won't be out soon. > > > I'm actually surprised that it hasn't propagated over to the servers yet > ... perhaps it will be there later today (noon-ish PST) or tomorrow > > Compiling and installing yourself is as easy as running "R CMD INSTALL > package_name" (depending on the os you are on) so I'd definitely recommend > you try that. > > You need to ensure you have a valid build tool gain on your machine that > includes gcc. If you are running osx or Linux, setting up a sane build > environment is quite easy. From what I understand, it is also relatively > easier to set this up on windows with newer versions of r (you should be on > 3.0.x anyway) ... So, I think you can give it a shot to see? > > -Steve > > > > Thanks again, > > Charles > > > > > > On Mon, Jul 15, 2013 at 3:45 PM, Steve Lianoglou > > <lianoglou.steve@gene.com <javascript:;="">>wrote: > > > > > Hi Charles, > > > > > > > > > On Mon, Jul 15, 2013 at 12:23 PM, Charles Determan Jr < > deter088@umn.edu<javascript:;> > > > > > > wrote: > > > > Greetings, > > > > > > > > I am trying to run an interaction formula with DESeq2. I try and run > > the > > > > following code and get the following error: > > > > > > > >> design(DESeq.cds) <- formula(~ subject+group+group:times)> DESeq.cds > > <- > > > DESeq(DESeq.cds)estimating size factorsestimating dispersionsyou had > > > estimated dispersions, replacing thesegene-wise dispersion > estimatesError > > > in modelMatrixNames[match(convertNames$from, modelMatrixNames)] <- > > > convertNames$to : > > > > NAs are not allowed in subscripted assignments > > > > > > > > > > > > I am not sure exactly what this means. I have uneven groups sizes > but > > it > > > > doesn't seem to be an issue when I have the design: > > > > > > > >> design(DESeq.cds) <- formula(~ subject+times+group+group:times) > > > > > > > > > > > > But the above formula doesn't provide the contrasts I would like. I > > > would > > > > like to have the coefficients to be as follows so I can report how > the > > > > genes change in response in the different groups over time. > > > > > > This is related to my recent posting over @ bioc-devel which Mike just > > > committed a fix for: > > > > > > https://stat.ethz.ch/pipermail/bioc-devel/2013-July/004463.html > > > > > > The good news is that Mike has patched the current and devel versions, > > > so you should be able to get them soon once version 1.0.18 propagates > > > through the build system: > > > > > > https://stat.ethz.ch/pipermail/bioc-devel/2013-July/004503.html > > > > > > Or, optionally, you can d/l from SVN and compile/install yourself, if > > > you are equipped to do so. > > > > > > HTH, > > > -steve > > > > > > -- > > > Steve Lianoglou > > > Computational Biologist > > > Bioinformatics and Computational Biology > > > Genentech > > > > > > > > > > > -- > > Charles Determan > > Integrated Biosciences PhD Candidate > > University of Minnesota > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <javascript:;> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > Steve Lianoglou > Computational Biologist > Bioinformatics and Computational Biology > Genentech > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Jose M. Garcia Manteiga PhD Research Assistant - Data Analysis in Functional Genomics Center for Translational Genomics and BioInformatics Dibit2-Basilica, 3A3 San Raffaele Scientific Institute Via Olgettina 58, 20132 Milano (MI), Italy Tel: +39-02-2643-4751 e-mail: garciamanteiga.josemanuel@hsr.it [[alternative HTML version deleted]]