Question: limma 3-way interaction
0
gravatar for Jacob Michaelson
13.2 years ago by
Jacob Michaelson320 wrote:
Hi all, A while back I found some great code on the list to test for a two-way interaction in limma: > 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. > This code has worked very well for me. I hand-coded an interaction using contrasts and got the exact same results as with using the above code - which was encouraging. How could this code be adapted for a three-way interaction, ie: X=model.matrix(~a*b*c) Is it safe to just to substitute this line? Any help much appreciated! --Jake
safe • 445 views
ADD COMMENTlink modified 13.2 years ago • written 13.2 years ago by Jacob Michaelson320
Answer: limma 3-way interaction
0
gravatar for Jacob Michaelson
13.2 years ago by
Jacob Michaelson320 wrote:
Okay I think I get it now. I couldn't figure out what the "assign" part was for. It refers to the term in the expanded formula which led to the term(s) you're interested in, for example: a*b -> Y = int + a + b + ab 0 1 2 3 hence the line cont.ia <- diag(p)[,attr(X,"assign")==3] so for a three-way interaction it would be: a*b*c -> Y = int + a + b + c + ab + ac + bc + abc 0 1 2 3 4 5 6 7 so the line would change to cont.ia <- diag(p)[,attr(X,"assign")==7] Am I interpreting this right? --Jake On Thu, 2006-05-18 at 09:22 -0600, Jake wrote: > Hi all, > > A while back I found some great code on the list to test for a two- way > interaction in limma: > > > 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. > > > > This code has worked very well for me. I hand-coded an interaction > using contrasts and got the exact same results as with using the above > code - which was encouraging. > > How could this code be adapted for a three-way interaction, ie: > > X=model.matrix(~a*b*c) > > Is it safe to just to substitute this line? > > Any help much appreciated! > > --Jake > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 13.2 years ago by Jacob Michaelson320
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 304 users visited in the last hour