SEQanswers Limma multifactor experiment design matrix
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 10-17-2016, 03:45 PM #1 Lugalbanda Junior Member   Location: Canada Join Date: Oct 2016 Posts: 3 Limma multifactor experiment design matrix Hi, so I am very confused as to how I can make a multifactor design for limma RNA differential expression. I've read other posts in different forums and none of the answers are very explicit (to me) as to how to build a multifactor design For examples, say I have p1N, p1T, p2N, and p2T, where p# is patient number and N/T is normal tumor. I can build a single factor design matrix like this: ------Normal------Tumor 1 ------ 1 --------- 0 2 ------ 0 --------- 1 3 ------ 1 --------- 0 4 ------ 0 --------- 1 I am completely lost as to how I can build a numeric matrix with multiple factors, which in this case, the factors would be patient number and N/T.
 10-17-2016, 11:33 PM #2 dpryan Devon Ryan   Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480 Code: ```d = data.frame(patient=factor(c("p1", "p1", "p2", "p2", ...)), condition=factor(c("N", "T", "N", "T", ...))) design = model.matrix(~patient + condition, d)``` N.B., I've likely made a typo somewhere, but that's the gist.
 10-18-2016, 09:21 AM #3 Lugalbanda Junior Member   Location: Canada Join Date: Oct 2016 Posts: 3 Oh, I thought I had to manually build a numeric matrix for the design matrix. Thanks. I have a followup question. I understand that the intercept column that is resulted is used for pair wise comparison. My question is when to use: design = model.matrix(~0+patient + condition, d) as opposed to this design = model.matrix(~patient + condition, d) Ok I found this from another post: EDIT: "This [design = model.matrix(~0+patient + condition, d)] (a cell means model) simply computes the mean expression for each group, and then you have to make all contrasts explicitly. The [design = model.matrix(~patient + condition, d)] has an implicit contrast (everything is a comparison to control), so you have to make contrasts for some comparisons, but not for others." from https://support.bioconductor.org/p/57268/ So is it safe to say this only matters if I am doing a contrast matrix comparison? Last edited by Lugalbanda; 10-18-2016 at 09:35 AM.
 10-19-2016, 12:12 AM #4 dpryan Devon Ryan   Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480 Correct, the "0+" is only needed if you want to specify contrasts, which aren't needed to answer your question.

 Tags differential expression, limma voom