Re: Equivalent of contrasts.fit & multi-contrast decideTests for edgeR?

Dear Gordon,

That is great to hear. I've just updated, and I see the new changes are 
in place. I'll be testing them out this week.

Thanks for adding this.

-Ryan

On Sat 08 Dec 2012 04:15:32 PM PST, Gordon K Smyth wrote:
> Dear Ryan,
>
> The edgeR glmLRT() function now allows the contrast to be a matrix
> with multiple columns.  The behavior of this argument is now analogous
> to the coef argument.  When multiple contrasts (or multiple coefs) are
> specified, the LR tests are conducted for all the contrasts at once,
> i.e., the LRTs are on several degrees of freedom, one for each
> independent contrast.
>
> This extension allows very general access to anova-type tests using
> edgeR.
>
> I committed this change to the official release of edgeR yesterday.
>
> Best wishes
> Gordon
>
> ---------------------------------------------
> Professor Gordon K Smyth,
> Bioinformatics Division,
> Walter and Eliza Hall Institute of Medical Research,
> 1G Royal Parade, Parkville, Vic 3052, Australia.
> http://www.statsci.org/smyth
>
> On Tue, 20 Nov 2012, Gordon K Smyth wrote:
>
>> Dear Ryan,
>>
>> It is true that glmLRT() does not allow you to specify multiple
>> contrast vectors to get an F-like test.  There is no good reason for
>> this other than that we haven't got around to it yet.  We will by the
>> next Bioconductor release.
>>
>> The fact that decideTestsDGE doesn't work with multiple coefficients
>> is unavoidable.  Note that decideTests() in limma doesn't give
>> results for F-tests either, only for individual contrasts.  The basic
>> difference between linear models and glms is that with linear models,
>> the F-test and all the individual t-tests that make it up can be
>> conducted as one computation, but for glms each individual 1df test
>> and the overall F-test have to all be separate computations.  This is
>> why we ask you to do multiple calls to glmLRT() to test for lots of
>> different contrasts, whereas limma can test for any number of
>> contrasts in one step.
>>
>> Best wishes
>> Gordon
>>
>> --------------- original message --------------
>>
>> [BioC] Equivalent of contrasts.fit & multi-contrast decideTests for
>> edgeR?
>> Ryan C. Thompson rct at thompsonclan.org
>> Tue Nov 20 02:26:37 CET 2012
>>
>> Hi all,
>>
>> I am trying to compare limma (with voom) and edgeR for RNA-seq
>> differential expression analysis, and I have noticed that while edgeR's
>> glm functionality closely matches the functionality of limma, one
>> feature seems to be missing: testing of multiple contrasts.
>> Specifically:
>>
>> 1. In glmLRT, the contrast argument only takes a single contrast, not a
>> matrix of contrasts (as limma's contrasts.fit would);
>> 2. If glmLRT is used with a coef argument containing 2 or more coefs,
>> then decideTestsDGE cannot handle the resulting object.
>>
>> To illustrate what I mean with an example, consider the following
>> experimental design with 3 replicates each of 3 timepoints, where I fit
>> the same data with two equivalent design matrices, one with an intercept
>> term and one without:
>>
>> library(edgeR)
>> dge <- DGEList(...) # Imagine data here
>> sampledata <- data.frame(timepoint=,
>>                          )
>> timepoint <- rep(factor(c("T0", "T1", "T2", "T3")), each=3)
>> design <- model.matrix(~timepoint)
>> design.noint <- model.matrix(~0+timepoint)
>> fit <- glmFit(dge, design)
>> fit.noint <- glmFit(dge, design.noint)
>> ## Test for changes in any timepoint
>> lrt.any.changes <- glmLRT(fit, coef=c(2,3,4))
>> ## How can this test be performed on fit.noint?
>> lrt.any.changes <- glmLRT(fit.noint, ???)
>> ## This throws an error because the DGELRT has multiple columns
>> ## "logFC.*" instead of just a single "logFC" that the function
>> ## expects.
>> decideTestsDGE(lrt.any.changes)
>>
>>
>> By contrast, with limma I can always do the test that I want regardless
>> of how I choose to parametrize my design matrix (intercept or not):
>>
>> library(limma)
>> ## Equivalent procedure in limma (I think)
>> lfit <- lmFit(voom(dge, design))
>> lfit.noint <- lmFit(voom(dge, design.noint))
>> ## Test for changes in any timepoint (result is in $F.p.value)
>> lfit <- eBayes(lfit)
>> ## Same test on the version with no intercept term
>> contrasts.anychange.noint <- makeContrasts(timepointT1-timepointT0,
>>                                            timepointT2-timepointT0,
>>                                            timepointT3-timepointT0,
>>                                            levels=design.noint)
>> lfit.noint <- eBayes(contrasts.fit(lfit.noint))
>> ## Should give identical results?
>> decideTests(lfit)
>> decideTests(lfit.noint)
>>
>> Basically, I far as I can tell, with edgeR you can test the null
>> hypothesis of multiple model coefficients being zero, but not multiple
>> contrasts, despite the fact that both procedures should be statistically
>> equivalent. Is edgeR missing this functionality or am I missing the
>> proper way to do it? Not having this functionality makes things a little
>> confusing, because depending on which one of several equivalent
>> parametrizations I choose, different tests are available or not
>> available, as illustrated by the code above, in which I can only test
>> the hypothesis of "any change between any time points" if I include an
>> intercept term. If I'm missing something, can someone pleas enlighten
>> me? If edgeR really is missing this functionality, is it planned for the
>> future or is there some fundamental difference between lms and glms that
>> makes it impossible?
>>
>> Thanks,
>>
>> -Ryan Thompson
>>
>
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