Dear All, Could you please help me to design a contrast for Differential Analysis? .... constrast.matrix <- makeContrasts ( --------, levels=design) ... I have 4 groups. A - normal B - cancer C - normal + drug D - cancer + drug I would like to find genes modulated in D versus C. These genes should be not affected or change significantly in B versus A Any suggestion? Many thanks, Paolo [[alternative HTML version deleted]]

Dear Paolo, sounds like you want: (D - C) - (B - A) Cheers, - axel On Tue, Apr 15, 2014 at 9:16 AM, Paolo Kunderfranco < paolo.kunderfranco@gmail.com> wrote: > Dear All, > > Could you please help me to design a contrast for Differential Analysis? > > .... > constrast.matrix <- makeContrasts ( > --------, > levels=design) > ... > > > I have 4 groups. > > A - normal > B - cancer > C - normal + drug > D - cancer + drug > > I would like to find genes modulated in D versus C. These genes should be > not affected or change significantly in B versus A > > > Any suggestion? > > Many thanks, > > Paolo > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Axel Klenk Research Informatician Information Management Drug Discovery Actelion Pharmaceuticals Ltd. * Gewerbestrasse 16 * CH-4123 Allschwil * Switzerland G12.O1.R10 VOIP 92 63 67 * phone +41 61 565 63 67 axel.klenk@actelion.com * www.actelion.com Address for visitors: Hegenheimermattweg 91 -- The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com [[alternative HTML version deleted]]