Question

lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions

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pecot • 0

@pecot-13903

Last seen 7.3 years ago

Hi,

I'm using deseq2 for a RNAseq experiment with 2 genotypes and 5 conditions (2 replicates for each combination of genotype and condition). When I use the deseq command to perform a comparison, I get different results if all experiments are in the DESeqDataSet than when only the 2 compared experiments are in the DESeqDataSet, what is expected as the estimation steps for the model parameters look at all the samples in the DESeqDataSet. Then, if I try to apply lfcShrink with the DESeqDataSet with all experiments, it takes forever. I've waited for 24 hours and still no results. As I have many comparisons, this is not an option. Same thing with rlog. Is it normal? How should I proceed?

Thanks,

Thierry

deseq2 lfcshrink rlog • 2.1k views

ADD COMMENT • link 7.3 years ago pecot • 0

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I haven't tried on another machine, but if it works on yours, it means that mine has a problem. I fully reinstalled R and remove all libraries, reinstalled DESeq2, still the same... I suspect something more vicious, maybe related to GCC compiler or C++ libraries. I'll have a look at it next week, here everything is closing with Irma coming. I'll let you know when I find a solution, if I find one (hope so :).

ADD REPLY • link 7.3 years ago pecot • 0

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Sorry, I didn't have the opportunity to work on it. Everything shut down here because of Irma.

I worked on a machine with Ubuntu 14.4. I tried to reinstall all packages and R, but nothing changed. I have the feeling that it's related to GCC as it says when I install DESeq2 that openMP is not working while I have gcc-4.8 and gcc-4.9 (default) installed on my computer, both enabling the use of openMP. I tried to find a way to tell R which gcc to use, but it's really not clear how it works and I couldn't find a way to do it properly. I have a virtualbox with Windows 10 so I installed R on it and I'm now able to run lfcShrink normally. It's great in the sense that I'm not stuck and I can analyze the data I have, but it's frustrating not to be able to understand why it's not working with Ubuntu. Do you have any idea?

ADD REPLY • link 7.3 years ago pecot • 0

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Sorry, no ideas...

ADD REPLY • link 7.3 years ago Michael Love 43k

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No worries, I found a way to make it work. I'll try it again when I upgrade to Ubuntu 16, never knows.

ADD REPLY • link 7.3 years ago pecot • 0

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I upgraded to Ubuntu 16 and ... it works!!!!!!!!!

I can't tell why it works now, but it might be helpful for others. Michael, thanks a lot for your comments!

ADD REPLY • link 7.3 years ago pecot • 0

score 0 · Answer 1 · 2017-09-06

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Michael Love 43k

@mikelove

Last seen 3 days ago

United States

2 * 5 * 2 = 20 samples should take at most a few minutes. Something is wrong. Can you send me the 'dds' to the email address found at maintainer("DESeq2")?

ADD COMMENT • link 7.3 years ago Michael Love 43k

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I'd recommend using vst() for variance stabilization and then making PCA plots or heatmaps. Not sure why you are experiencing more than a minute with lfcShrink:

> system.time({ vsd <- vst(dds, blind=FALSE) })
   user  system elapsed
  2.942   0.116   3.108

> system.time({
+ res <- results(dds, contrast=c("condition","US.RbKO","US.Wt"))
+ res <- lfcShrink(dds, contrast=c("condition","US.RbKO","US.Wt"), res=res)
+ })
   user  system elapsed
 51.153   1.309  53.800

I'm using DESeq2 v1.17 which is similar to the current release v1.16.

ADD REPLY • link 7.3 years ago Michael Love 43k

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With just 'results', I get this:

system.time({
+ res <- results(dds, contrast=c("condition","US.RbKO","US.Wt"))
+ })
user system elapsed
10.996 43.532 6.956

I tried 'lfcShrink':

system.time({
+ res <- lfcShrink(dds, contrast=c("condition","US.RbKO","US.Wt"), res=res)
+ })

It's been running for 15 minutes and still no results. With a similar comparison, I let 'lfcShrink' run over the night and I got no results. I guess it's more a system problem. Do you have any idea?

ADD REPLY • link 7.3 years ago pecot • 0

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That's definitely strange. Can you try on another machine? And/or try reinstalling DESeq2?

If it takes more than 5 minutes, don't bother waiting longer, it's a problem with the installation I would say.

Above is running on a laptop using 1 core.

ADD REPLY • link 7.3 years ago Michael Love 43k