Hi, reading the BioC list I see that things like this are asked often, but I am sorry I just can't get this. Could somebody show me how to do it: I have a microarray experiment with 2 strains and 3 time points from each, so I would like to do 2x3 factorial experiment to get all the genes that change in strain A (or B) during time series (10, 30, 60 min) and between strains in all the time points. So trying to follow limma guide, the design matrix object would be something like this (with 2 repeats for each): > dQex (Intercept) Qexa10 Qexa30 Qexa60 Qexb10 Qexb30 1 1 1 0 0 0 0 2 1 1 0 0 0 0 3 1 0 1 0 0 0 4 1 0 1 0 0 0 5 1 0 0 1 0 0 6 1 0 0 1 0 0 7 1 0 0 0 1 0 8 1 0 0 0 1 0 9 1 0 0 0 0 1 10 1 0 0 0 0 1 11 1 0 0 0 0 0 12 1 0 0 0 0 0 attr(,"assign") [1] 0 1 1 1 1 1 attr(,"contrasts") attr(,"contrasts")$Qex a10 a30 a60 b10 b30 a10 1 0 0 0 0 a30 0 1 0 0 0 a60 0 0 1 0 0 b10 0 0 0 1 0 b30 0 0 0 0 1 b60 0 0 0 0 0 What kind of contrast (or as well design) matrix do I need to get all the changing genes out? Cheers, Mikko Mikko Arvas VTT Biotechnology Please note new tel/fax number from start of year 2005. e-mail: mikko.arvas@vtt.fi tel: +358-(0)20-722 5827 mobile: +358-(0)44-381 0502 fax: +358 20 722 7071 mail: Tietotie 2, Espoo P.O. Box 1500 FIN-02044 VTT, Finland Protein production group's website: http://www.vtt.fi/bel/bpro/proteinprod/indexe.htm

> Date: Wed, 04 May 2005 17:37:35 +0300 > From: Mikko Arvas <mikko.arvas@vtt.fi> > Subject: [BioC] factorial experiment matrix design > To: bioconductor@stat.math.ethz.ch > > Hi, > > reading the BioC list I see that things like this are asked often, but I am > sorry I just can't get this. Could somebody show me how to do it: > > I have a microarray experiment with 2 strains and 3 time points from each, > so I would like to do 2x3 factorial experiment > to get all the genes that change in strain A (or B) during time series (10, > 30, 60 min) and between strains in all the time points. > > So trying to follow limma guide, the design matrix object would be > something like this (with 2 repeats for each): > > > dQex > (Intercept) Qexa10 Qexa30 Qexa60 Qexb10 Qexb30 > 1 1 1 0 0 0 0 > 2 1 1 0 0 0 0 > 3 1 0 1 0 0 0 > 4 1 0 1 0 0 0 > 5 1 0 0 1 0 0 > 6 1 0 0 1 0 0 > 7 1 0 0 0 1 0 > 8 1 0 0 0 1 0 > 9 1 0 0 0 0 1 > 10 1 0 0 0 0 1 > 11 1 0 0 0 0 0 > 12 1 0 0 0 0 0 > attr(,"assign") > [1] 0 1 1 1 1 1 > attr(,"contrasts") > attr(,"contrasts")$Qex > a10 a30 a60 b10 b30 > a10 1 0 0 0 0 > a30 0 1 0 0 0 > a60 0 0 1 0 0 > b10 0 0 0 1 0 > b30 0 0 0 0 1 > b60 0 0 0 0 0 > > What kind of contrast (or as well design) matrix do I need to get all the > changing genes out? YOu need to pick out the 5 non-intercept coefficients: cont.matrix <- rbind(0,diag(5)) Gordon > Cheers, > Mikko > > > > Mikko Arvas > VTT Biotechnology > > Please note new tel/fax number > from start of year 2005. > > e-mail: mikko.arvas@vtt.fi > tel: +358-(0)20-722 5827 > mobile: +358-(0)44-381 0502 > fax: +358 20 722 7071 > mail: Tietotie 2, Espoo > P.O. Box 1500 > FIN-02044 VTT, Finland > > Protein production group's website: > http://www.vtt.fi/bel/bpro/proteinprod/indexe.htm