I am using your package (which is great!) but I have a question. I have a table with individuals that have two more groups beside the condition column: like sex and population. Could I put as formula ~ conditions +sex +population, and when I retrieve the results from Condition, will I get only DE genes that are due to the condition and not due to sex or population? cheers Lo On Tue, Jun 18, 2013 at 1:34 PM, Michael Love <michaelisaiahlove@gmail.com>wrote: > hi, > > Could you please email me and CC the bioconductor list, in case your > question is relevant to some other users? > > thanks, > > Mike > > On Tue, Jun 18, 2013 at 1:30 PM, Lorena Pantano <lorena@vpantano.name> > wrote: > > Hi, > > > > I am using your package, which is great! but I have a question. > > > > I have a table with individuals that have two more groups beside the > > condition column: like sex and population. Could I put as formula ~ > > conditions +sex +population, and when I retrieve the results from > Condition, > > will I get only DE genes that are due to the condition and not due to > sex or > > population? > > > > Thanks a lot in advance, if this is possible I can avoid to run DESeq > > multiple times > > > > thanks again > > > > > > Lorena Pantano > > Post-doctoral Researcher > > Regulatory Genomics Group > > Institut de Medicina Predictiva i Personalitzada del Càncer > > http://vpantano.name > [[alternative HTML version deleted]]

hi Lorena, On Tue, Jun 18, 2013 at 1:40 PM, Lorena Pantano <lorena.pantano at="" gmail.com=""> wrote: > I have a table with individuals that have two more groups beside the > condition column: like sex and population. Could I put as formula ~ > conditions +sex +population, and when I retrieve the results from Condition, > will I get only DE genes that are due to the condition and not due to sex or > population? > Yes, you can use a design formula like you have written to control for sex and population, and then retrieve the results for only the 'condition' variable. Better would be to put 'condition' at the end of the design, so that it is the default variable used by results() and plotMA(). The results function has an argument 'name', which specifies which variable+factor-level which should be used for constructing the results DataFrame. By default, the last factor level of the last variable is used. This is discussed in the vignette and in the man page for results(). The resultsNames() function will return the possible names which you can supply to the 'name' argument of results(): resultsNames(dds) -Mike