Thanks Steve, Had a quick look and it seems like it might be it! I am looking forward to read the paper! Thanks for the suggestion! Christian -----Original Message----- From: mailinglist.honeypot@gmail.com [mailto:mailinglist.honeypot@gmail.com] On Behalf Of Steve Lianoglou Sent: 11 March 2014 16:38 To: Christian De Santis Cc: bioconductor at r-project.org Subject: Re: [BioC] Finding genes with similar trend Hi, On Tue, Mar 11, 2014 at 9:26 AM, Christian De Santis <christian.desantis at="" stir.ac.uk=""> wrote: > Dear List, > > I have data from a nutritional microarray experiment with 5 treatments where one component of the diet is varying in different proportions. > I have visually identified some genes that in my opinion share a common and possibly interesting trend. However, I was wondering if it exists a way to model this trend and extract other genes from the list that fit this trend. It is not necessarily a linear increase or decrease of expression (I know how to do that in Limma). > > Perhaps anyone is aware of any functions of existing packages that can perform such a task? Thanks very much for your help, as usual! Are you looking to do something like what the voom folks did in Figure 11 of their paper: voom: precision weights unlock linear model analysis tools for RNA-seq read counts http://genomebiology.com/2014/15/2/R29 This is a direct link to the figure: http://genomebiology.com/2014/15/2/R29/figure/F11 If so, I reckon reading the paper + methods should give you a good idea about how to start. HTH, -steve -- Steve Lianoglou Computational Biologist Genentech -- The University of Stirling has been ranked in the top 12 of UK universities for graduate employment*. 94% of our 2012 graduates were in work and/or further study within six months of graduation. *The Telegraph The University of Stirling is a charity registered in Scotland, number SC 011159.