Hi there, I was wondering what command to use to see the lists of genes for group3-group2 and group3-group1. In the example from the user guide the top genes expressed differentially in group2 versus group1 can be obtained with the command listed below. I have tried to extrapolate this to get the other contrasts, but have had no success. To make all pair-wise comparisons between the three groups the appropriate contrast matrix can be created by > contrast.matrix <- makeContrasts(group2-group1, group3-group2, group3-group1, levels=design) > fit2 <- contrasts.fit(fit, contrast.matrix) > fit2 <- eBayes(fit2) A list of top genes differential expressed in group2 versus group1 can be obtained from > topTable(fit2, coef=1, adjust="fdr") Any help on this matter would be greatly appreciated. Regards, Jeremy. Jeremy Preston, PhD Applications Scientist Millennium Science <http: www.mscience.com.au=""> www.mscience.com.au 2/390 Canterbury Road, Surrey Hills, Victoria 3127 Australia mob: 0407 742 426 | office: +61 3 9830 7922 | fax: +61 3 9830 7933 jpreston@mscience.com.au support@mscience.com.au [[alternative HTML version deleted]]

In your example, topTable(fit2, coef=1, adjust="fdr") Will get you the diff expressed genes for "group2-group1". topTable(fit2, coef=2, adjust="fdr") Will get you the genes for "group3-group2" etc The key argument here is "coef", which you should use to refer to the index of the coefficient as specified in the call to makeContrasts. Mick -----Original Message----- From: Jeremy Preston [mailto:jpreston@mscience.com.au] Sent: 19 November 2004 06:03 To: bioconductor@stat.math.ethz.ch Subject: [BioC] help with limma commands Hi there, I was wondering what command to use to see the lists of genes for group3-group2 and group3-group1. In the example from the user guide the top genes expressed differentially in group2 versus group1 can be obtained with the command listed below. I have tried to extrapolate this to get the other contrasts, but have had no success. To make all pair-wise comparisons between the three groups the appropriate contrast matrix can be created by > contrast.matrix <- makeContrasts(group2-group1, group3-group2, group3-group1, levels=design) > fit2 <- contrasts.fit(fit, contrast.matrix) > fit2 <- eBayes(fit2) A list of top genes differential expressed in group2 versus group1 can be obtained from > topTable(fit2, coef=1, adjust="fdr") Any help on this matter would be greatly appreciated. Regards, Jeremy. Jeremy Preston, PhD Applications Scientist Millennium Science <http: www.mscience.com.au=""> www.mscience.com.au 2/390 Canterbury Road, Surrey Hills, Victoria 3127 Australia mob: 0407 742 426 | office: +61 3 9830 7922 | fax: +61 3 9830 7933 jpreston@mscience.com.au support@mscience.com.au [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor