[BioC] DEseq() takes extremely long time
Dong, Xianjun
XDONG at rics.bwh.harvard.edu
Tue Apr 15 00:48:06 CEST 2014
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
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