DEseq() takes extremely long time
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@mikelove
Last seen 14 hours ago
United States
hi Xianjun, This should be fixed in the newly released version 1.4. We often recommend turning continuous variables into factors. Especially something like age, where we don't typically hypothesize that the gene expression will double every x years. Breaking it up into 3-5 meaningful groups often makes more sense. However, with dosage or some other covariates, supposing a linear trend (in the log2 space) might make sense. Mike On Mon, Apr 14, 2014 at 6:48 PM, Dong, Xianjun <xdong at="" rics.bwh.harvard.edu=""> wrote: > Hi Mike, > > I was applying DEseq() function to dds (as below) for all human genes, and the script is stalled at the step of ?gene-wise dispersion estimates" for >1 hours. Do you have clue for the reason? Should I convert all covariances into factor? > > p.s. sessionInfo() attached. > > -Xianjun > >> dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, > + directory = input_dir, > + design= ~ condition + batch + cellType + age + sex + RIN + PMI) >> colData(dds)$condition <- factor(colData(dds)$condition, levels=c("HC?,"Treament1", "Treament2")) >> dds <- DESeq(dds) > estimating size factors > estimating dispersions > gene-wise dispersion estimates > > ================== sessionInfo() ================ > >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] DESeq2_1.2.10 RcppArmadillo_0.3.930.1 Rcpp_0.11.1 > [4] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.7 > [7] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] annotate_1.40.0 AnnotationDbi_1.24.0 Biobase_2.22.0 > [4] DBI_0.2-7 genefilter_1.44.0 grid_3.0.1 > [7] lattice_0.20-24 locfit_1.5-9.1 RColorBrewer_1.0-5 > [10] RSQLite_0.11.4 splines_3.0.1 stats4_3.0.1 > [13] survival_2.37-4 XML_3.98-1.1 xtable_1.7-1 > > > > The information in this e-mail is intended only for th...{{dropped:13}}
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Entering edit mode
Xianjun Dong ▴ 30
@xianjun-dong-6382
Last seen 9.7 years ago
United States
Hi Mike, I was applying DEseq() function to dds (as below) for all human genes, and the script is stalled at the step of ?gene-wise dispersion estimates" for >1 hours. Do you have clue for the reason? Should I convert all covariances into factor? p.s. sessionInfo() attached. -Xianjun > dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, + directory = input_dir, + design= ~ condition + batch + cellType + age + sex + RIN + PMI) > colData(dds)$condition <- factor(colData(dds)$condition, levels=c("HC?,"Treament1", "Treament2")) > dds <- DESeq(dds) estimating size factors estimating dispersions gene-wise dispersion estimates ================== sessionInfo() ================ > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] DESeq2_1.2.10 RcppArmadillo_0.3.930.1 Rcpp_0.11.1 [4] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.7 [7] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] annotate_1.40.0 AnnotationDbi_1.24.0 Biobase_2.22.0 [4] DBI_0.2-7 genefilter_1.44.0 grid_3.0.1 [7] lattice_0.20-24 locfit_1.5-9.1 RColorBrewer_1.0-5 [10] RSQLite_0.11.4 splines_3.0.1 stats4_3.0.1 [13] survival_2.37-4 XML_3.98-1.1 xtable_1.7-1 The information in this e-mail is intended only for the ...{{dropped:11}}
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