[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. 


> 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)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=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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