Question: lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions
gravatar for pecot
15 days ago by
pecot0 wrote:



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?





ADD COMMENTlink modified 7 days ago • written 15 days ago by pecot0

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 REPLYlink written 13 days ago by pecot0

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 REPLYlink written 7 days ago by pecot0

Sorry, no ideas...

ADD REPLYlink written 7 days ago by Michael Love13k

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

ADD REPLYlink written 7 days ago by pecot0

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 REPLYlink written 1 day ago by pecot0
gravatar for Michael Love
15 days ago by
Michael Love13k
United States
Michael Love13k wrote:

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 COMMENTlink written 15 days ago by Michael Love13k

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 REPLYlink written 14 days ago by Michael Love13k

With just 'results', I get this:

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

I tried 'lfcShrink':

+ 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 REPLYlink written 14 days ago by pecot0

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 REPLYlink written 14 days ago by Michael Love13k
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