Deseq2 , result() taking too long > 3hrs
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Nidhi • 0
@628d58c8
Last seen 8 weeks ago
United States

I ran deseq on 8 samples, which took about 30-45mins. But on running results(), it's been more than 3 hours and still running. I can hear my laptop buzzing.

dd_cc1=DESeq(dds_CC)

estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

res.cc=results(dds_cc1,contrast = c("sex","male","female"))


sessionInfo( )

Thoughts?

DESeq2 • 293 views
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It ran faster if I filtered the table based on reads. So it works, but it's just being slow with larger datasets

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@mikelove
Last seen 14 hours ago
United States

Something is off. It should take a few seconds. It should be linear with number of genes.

> dds <- makeExampleDESeqDataSet(n=1e4, m=8)
> system.time({ DESeq(dds) })
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
   user  system elapsed
  1.362   0.030   1.402
> dds <- DESeq(dds, quiet=TRUE)
> system.time({ results(dds) })
   user  system elapsed
  0.077   0.005   0.083

> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.0.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
 [1] DESeq2_1.38.1               SummarizedExperiment_1.28.0 Biobase_2.58.0
 [4] MatrixGenerics_1.10.0       matrixStats_0.63.0          GenomicRanges_1.50.1
 [7] GenomeInfoDb_1.34.4         IRanges_2.32.0              S4Vectors_0.36.0
[10] BiocGenerics_0.44.0
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