Question: Re: F-tests for factorial effects - limma

0

Ramon Diaz •

**1.1k**wrote:Dear Naomi and Gordon,
Just in case it helps someone else, I am attaching a more verbose
version of
the code snippet that Gordon sent, because I found the "diag(p)
[,attr(X,"assign")==3]" non-intuitive, so I called makeContrasts
explicitly.
This is the example:
*****************************************************************
## treat is a factor with three levels; age is a continuous variable.
X <- model.matrix( ~ treat*age.centered)
fit <- lmFit(d.clean, X)
p <- ncol(X)
cont.ia <- diag(p)[,attr(d.trt.BY.age3,"assign")==3]
fit.ia <- eBayes(contrasts.fit(fit, cont.ia))
############# Using my more verbose apporach
X2 <- model.matrix( ~ treat*age.centered)
colnames(X2) <- c("Intercept", "Colon", "Mama",
"age", "Colon.by.age", "Mama.by.age")
contrasts.trt.BY.age <- makeContrasts(Colon.by.age,
Mama.by.age,
levels = X2)
fit2 <- lmFit(d.clean, X2)
fit.ia2 <- eBayes(contrasts.fit(fit2,
contrasts.trt.BY.age))
### We can of course do instead (which I like better)
X2 <- model.matrix(~ -1 + treat + age.centered +
treat*age.centered)
colnames(X2) <- c("Colon", "Mama", "Normal",
"age", "Colon.by.age", "Mama.by.age")
contrasts.trt.BY.age <- makeContrasts(Colon.by.age,
Mama.by.age,
levels = X2)
*************************************************
Best,
R.
On Wednesday 22 December 2004 14:23, Gordon K Smyth wrote:
> > Date: Tue, 21 Dec 2004 17:21:19 -0500
> > From: Naomi Altman <naomi@stat.psu.edu>
> > Subject: [BioC] F-tests for factorial effects - limma
> > To: bioconductor@stat.math.ethz.ch
> >
> > I am analyzing a 2-factor factorial Affy experiment, with 3 d.f.
for each
> > factor.
> >
> > I would like to get the F-tests for the main effects and
interactions
> > using limma.
> >
> > I have computed all the contrasts, and got the t-tests (both
unadjusted
> > and eBayes). I do know how to combine these into F-tests "by
hand" but I
> > could not figure out if there was a simple way to do this using
limma.
>
> limma doesn't have any easy way to deal with main effects and
interactions,
> at least not with main effects, interactions are actually simpler.
I
> haven't implemented this because I've never been able to figure out
what
> one would do with these things in a microarray context.
>
> To compute F-tests for main effects and interaction, the easiest way
would
> probably be to compute the SS for main effects and interactions by
> non-limma means, then use shrinkVar() to adjust the residual mean
squares,
> i.e., the F-statistic denominators.
>
> If you only want F-tests for interactions, the following code would
work:
>
> X <- model.matrix(~a*b)
> fit <- lmFit(eset, X)
> p <- ncol(X)
> cont.ia <- diag(p)[,attr(X,"assign")==3]
> fit.ia <- eBayes(contrasts.fit(fit, cont.ia))
>
> Now fit.ia contains the F-statistic and p-values for the interaction
in
> fit.ia$F and fit.ia$F.p.value.
>
> > I had a look at FStat (classifyTestsF). There seems to be a
problem, in
> > that the matrix tstat is not premultiplied by the contrast matrix
when
> > the F-statistics are computed. So, if the contrasts are not full-
rank,
> > an error is generated (instead of the F-statistics) because
nrow(Q) !=
> > ncol(tstat).. (See the lines below).
>
> No, the code is correct. FStat is quite happy with non full rank
contrasts
> but the contrast matrix must be applied using contrasts.fit() before
> entering FStat(). You should not expect to see a contrast matrix
inside
> the classifyTestsF() code.
>
> Gordon
>
> > if (fstat.only) {
> > fstat <- drop((tstat%*% Q)^2 %*% array(1, c(r, 1)))
> > attr(fstat, "df1") <- r
> > attr(fstat, "df2") <- df
> > return(fstat)
> > }
> >
> > I figured that before I fiddled with the code, I would check to
make sure
> > that I didn't miss an existing routine to do this.
> >
> > Thanks in advance.
> >
> > Naomi S. Altman 814-865-3791
(voice)
> > Associate Professor
> > Bioinformatics Consulting Center
> > Dept. of Statistics 814-863-7114
(fax)
> > Penn State University 814-865-1348
(Statistics)
> > University Park, PA 16802-2111
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
Ram?n D?az-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncol?gicas (CNIO)
(Spanish National Cancer Center)
Melchor Fern?ndez Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900
http://ligarto.org/rdiaz
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modified 14.1 years ago
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Naomi Altman •

**6.0k**• written 14.1 years ago by Ramon Diaz •**1.1k**