Question: Limma\'s roast() does not accept weigths in combination with block
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6.0 years ago by
Guest User12k
Guest User12k wrote:
Dear All, I am conducting enrichment tests using Limma's roast() function. As I am investigating RNA-Seq data, I have to introduce the weights calculated by voom(). Without a blocking variable, roast() runs without an itch but when I introduce a blocking variable (with or without correlation within blocks), roast() halts and returns "Can't use block with weights". Is the combination of weights and blocking variables in roast() generally impossible and if not, will it be possible in upcomming releases of limma? Thank you very much in advance, Moritz -- output of sessionInfo(): sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel splines stats graphics grDevices utils datasets [8] methods base other attached packages: [1] DESeq_1.12.0 lattice_0.20-15 locfit_1.5-9.1 Biobase_2.20.0 [5] BiocGenerics_0.6.0 statmod_1.4.17 edgeR_3.2.3 limma_3.16.5 loaded via a namespace (and not attached): [1] annotate_1.38.0 AnnotationDbi_1.22.6 compiler_3.0.1 [4] DBI_0.2-7 genefilter_1.42.0 geneplotter_1.38.0 [7] grid_3.0.1 IRanges_1.18.1 RColorBrewer_1.0-5 [10] RSQLite_0.11.4 stats4_3.0.1 survival_2.37-4 [13] tools_3.0.1 XML_3.98-1.1 xtable_1.7-1 -- Sent via the guest posting facility at bioconductor.org.
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ADD COMMENTlink modified 6.0 years ago by Gordon Smyth37k • written 6.0 years ago by Guest User12k
Answer: Limma\'s roast() does not accept weigths in combination with block
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6.0 years ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:
> Date: Mon, 5 Aug 2013 03:36:49 -0700 (PDT) > From: "Moritz Hess [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, ssehztirom at gmail.com > Subject: [BioC] Limma\'s roast() does not accept weigths in > combination with block > > Dear All, > > I am conducting enrichment tests using Limma's roast() function. As I > am investigating RNA-Seq data, I have to introduce the weights > calculated by voom(). Without a blocking variable, roast() runs without > an itch but when I introduce a blocking variable (with or without > correlation within blocks), roast() halts and returns "Can't use block > with weights". Is the combination of weights and blocking variables in > roast() generally impossible Not impossible, but requires some careful special case programming. > and if not, will it be possible in upcomming releases of limma? Yes, but not in the next few weeks. Gordon > Thank you very much in advance, > > Moritz > > -- output of sessionInfo(): > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel splines stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] DESeq_1.12.0 lattice_0.20-15 locfit_1.5-9.1 Biobase_2.20.0 > [5] BiocGenerics_0.6.0 statmod_1.4.17 edgeR_3.2.3 limma_3.16.5 > > loaded via a namespace (and not attached): > [1] annotate_1.38.0 AnnotationDbi_1.22.6 compiler_3.0.1 > [4] DBI_0.2-7 genefilter_1.42.0 geneplotter_1.38.0 > [7] grid_3.0.1 IRanges_1.18.1 RColorBrewer_1.0-5 > [10] RSQLite_0.11.4 stats4_3.0.1 survival_2.37-4 > [13] tools_3.0.1 XML_3.98-1.1 xtable_1.7-1 > > > -- ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD COMMENTlink written 6.0 years ago by Gordon Smyth37k
Hi Gordon, thanks for your response. I appreciate very much to hear that this feature will be implemented in future releases of limma. Best regards, Moritz 2013/8/6 Gordon K Smyth <smyth@wehi.edu.au> > Date: Mon, 5 Aug 2013 03:36:49 -0700 (PDT) >> From: "Moritz Hess [guest]" <guest@bioconductor.org> >> To: bioconductor@r-project.org, ssehztirom@gmail.com >> Subject: [BioC] Limma\'s roast() does not accept weigths in >> combination with block >> >> Dear All, >> >> I am conducting enrichment tests using Limma's roast() function. As I am >> investigating RNA-Seq data, I have to introduce the weights calculated by >> voom(). Without a blocking variable, roast() runs without an itch but when >> I introduce a blocking variable (with or without correlation within >> blocks), roast() halts and returns "Can't use block with weights". Is the >> combination of weights and blocking variables in roast() generally >> impossible >> > > Not impossible, but requires some careful special case programming. > > and if not, will it be possible in upcomming releases of limma? >> > > Yes, but not in the next few weeks. > > Gordon > > Thank you very much in advance, >> >> Moritz >> >> -- output of sessionInfo(): >> >> sessionInfo() >> R version 3.0.1 (2013-05-16) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 >> [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel splines stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] DESeq_1.12.0 lattice_0.20-15 locfit_1.5-9.1 >> Biobase_2.20.0 >> [5] BiocGenerics_0.6.0 statmod_1.4.17 edgeR_3.2.3 limma_3.16.5 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.38.0 AnnotationDbi_1.22.6 compiler_3.0.1 >> [4] DBI_0.2-7 genefilter_1.42.0 geneplotter_1.38.0 >> [7] grid_3.0.1 IRanges_1.18.1 RColorBrewer_1.0-5 >> [10] RSQLite_0.11.4 stats4_3.0.1 survival_2.37-4 >> [13] tools_3.0.1 XML_3.98-1.1 xtable_1.7-1 >> >> >> -- >> > > ______________________________**______________________________**____ ______ > The information in this email is confidential and inte...{{dropped:25}}
ADD REPLYlink written 5.9 years ago by Moritz Hess60
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