[BioC] DESeq: Hypothesis testing in multifactor design
Yanzhu Lin
mlinyzh at gmail.com
Wed Aug 20 19:39:54 CEST 2014
Hi Mike,
So you mean I need to estimate the dispersions every time when I have a
different full model for LRT? In other words, so I need to use
estimateDispersions() once when I test the main effect, where the full
model is ~A+B+C, and use estimateDispersion() once when I test the
three-way interaction term, where the full model is
~A+B+C+A:B+A:C+B:C+A:B:C?
One more question about estimateDispersion(), does it take a very long time
to estimate the dispersions? I have 16649 features and 726 biosamples, and
I run the estimateDispersion function around 9:30 am this morning, and it
hasn't done yet. Any suggestion that I can speed up the
estimateDispesions().
Your help will be greatly appreciate, thanks.
Best,
On Wed, Aug 20, 2014 at 12:44 PM, Michael Love <michaelisaiahlove at gmail.com>
wrote:
> Hi Yanzhu,
>
> On Aug 20, 2014 3:59 PM, "Yanzhu Lin" <mlinyzh at gmail.com> wrote:
> >
> > Hi Mike,
> >
> > I am using DESeq2 package for my project now, and I have some questions
> regarding to this pacakge.
> >
> > Please let me briefly introduce some background information about my
> project. I have three factors: A with 16 levels, B with 2 levels and C with
> 3 levels, in total 16*2*3=96 groups. There are 8 biosamples for each group,
> hence 96*8=768 biosamples in total. Due to some issues, we lost some
> replicates for some groups, which ends up 726 biosamples, hence it is
> unbalance design.
> >
> > Our purpose are to test the main effects of three factor: A, B and C,
> the two-way interaction: A:B, A:C and B:C, and the three-way interaction
> term: A:B:C. For example, I will compare full model: ~A+B+C with reduce
> model: ~A+B to test factor C, and so on for other two main effects. For
> testing three-way interaction A:B:C, I will compare full model:
> ~A+B+C+A:B+A:C+B:C+A:B:C and reduced model ~A+B+C+A:B+A:C+B:C. Then come my
> questions.
> >
> >
> > I have different full models for testing main effects, two-way
> interaction and three-way interaction term. Will the dispersion estimation
> affected by my full model? Can I specify the full model when I use
> nbinomLRT()?
>
> No, you should not change the design in between, i.e. don't use a
> different design for dispersion estimation and the full model in the LRT.
>
> Mike
>
> > In other words, can I use estimateDispersion() only once and fit
> nbinomLRT with different full models as below:
> >
> >
> >
> dds<-DESeqDataSetFromMatrix(countData=countdata,colData=coldata,design=~A+B+C+A:B+A:C+B:C+A:B:C)
> >
> > ### normalization
> > dds=estimateSizeFactors(dds)
> >
> > ### dispersion estimation:
> > dds=estimateDispersions(dds)
> >
> > ###Test three-way interaction term.
> > dds<-nbinomLRT(dds,reduced=~A+B+C+A:B+A:C+B:C)
> > ###Test main effect of factor A:
> > dds<-nbinomLRT(dds,full=~A+B+C, reduced=~B+C)
> > ###Test main effect of factor B:
> > dds<-nbinomLRT(dds,full=~A+B+C, reduced=~A+C)
> >
> > ###Test main effect of factor C:
> > dds<-nbinomLRT(dds,full=~A+B+C, reduced=~A+B)
> >
> >
> > Thanks,
> >
> >
> > Yanzhu
> >
> >
> >
> >
> >
> > On Tue, Jun 10, 2014 at 4:07 PM, Michael Love <
> michaelisaiahlove at gmail.com> wrote:
> >>
> >> hi Yanzhu,
> >>
> >> Note that we recommend users switch to using DESeq2, which also has
> >> the likelihood ratio test you are using, and is faster and more
> >> sensitive.
> >>
> >> The pipeline would look like:
> >>
> >> DESeq(dds, test="LRT", reduced=~ A+B+C+A:B+A:C+B:C)
> >>
> >> for your first example.
> >>
> >> For your question, the terms of the reduced model should be contained
> >> within the full model. Still there are a number of models which
> >> satisfy this requirement, e.g. for testing B:C, you could use
> >> A+B+C+A:B+A:C+B:C and A+B+C+A:B+A:C as full and reduced respectively.
> >> Or you could use A+B+C+B:C and A+B+C. The importance of these other
> >> interaction terms depends on context, whether they are very
> >> explanatory or not.
> >>
> >> Mike
> >>
> >> On Tue, Jun 10, 2014 at 11:21 AM, yanzhu [guest] <
> guest at bioconductor.org> wrote:
> >> > Dear Community,
> >> >
> >> > I have a question about the hypothesis testing of the two-way
> interaction terms in a multifactor design which includes three factors: A,
> B and C.
> >> >
> >> > When I tested the three-way interaction I used the full and reduced
> models as below for nbinomGLMTest():
> >> > Full: count ~ A+B+C+A:B+A:C+B:C+A:B:C
> >> > Reduced: count ~ A+B+C+A:B+A:C+B:C
> >> >
> >> > Now comes my question, when I want to test the effect of two-way
> interaction terms, i.e., A:B, A:C or B:C, what should be my full and
> reduced models? For example, when I want to the test the effect of A:B,
> what should be my full and reduced models for nbinomGLMTest() using DESeq
> pacakge?
> >> >
> >> >
> >> > Best,
> >> >
> >> >
> >> >
> >> > Yanzhu
> >> >
> >> >
> >> > -- output of sessionInfo():
> >> >
> >> > sessionInfo()
> >> > R version 3.1.0 (2014-04-10)
> >> > Platform: x86_64-w64-mingw32/x64 (64-bit)
> >> >
> >> > locale:
> >> > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252 LC_MONETARY=English_United States.1252
> >> > [4] LC_NUMERIC=C LC_TIME=English_United
> States.1252
> >> >
> >> > attached base packages:
> >> > [1] parallel stats graphics grDevices utils datasets
> methods base
> >> >
> >> > other attached packages:
> >> > [1] DESeq_1.16.0 lattice_0.20-29 locfit_1.5-9.1
> Biobase_2.24.0 BiocGenerics_0.10.0 edgeR_3.6.1 limma_3.20.1
> >> >
> >> > loaded via a namespace (and not attached):
> >> > [1] annotate_1.42.0 AnnotationDbi_1.26.0 DBI_0.2-7
> genefilter_1.46.0 geneplotter_1.42.0 GenomeInfoDb_1.0.2
> >> > [7] grid_3.1.0 IRanges_1.22.6 MASS_7.3-31
> RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.1.0
> >> > [13] stats4_3.1.0 survival_2.37-7 tools_3.1.0
> XML_3.98-1.1 xtable_1.7-3
> >> >
> >> >
> >> > --
> >> > Sent via the guest posting facility at bioconductor.org.
> >> >
> >> > _______________________________________________
> >> > Bioconductor mailing list
> >> > Bioconductor at r-project.org
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> >
>
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