Page 51 of the edgeR User's Guide (4 May 2012) gives an example of this. Gordon On Mon, 4 Jun 2012, KJ Lim wrote: > Dear Prof Gordon, > > Thanks for your suggestion and explanation. > > How could I never thought about the expression (up or down- regulated) of > same genes may change when test on multiple coefficients! Thanks for your > time and help. Have a nice day. > > Best regards, > KJ Lim > > On 4 June 2012 04:11, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > >> Dear KJ Lim, >> >> When testing for multiple coefficients, the easiest way to learn the >> number of differentially expressed genes is by: >> >> FDR <- p.adjust(ltr$PValue, method="BH") >> sum(FDR < 0.05) >> >> There is however no unambiguous way to break this down by up and down >> genes. There is no unambiguous way to classify a gene as up or down with >> respect to multiple coefficients, because the coefficients may change in >> different directions for the same gene. >> >> Best wishes >> Gordon >> >> Date: Sat, 2 Jun 2012 18:19:32 +0300 >>> From: KJ Lim <jinkeanlim at="" gmail.com=""> >>> To: Bioconductor mailing list <bioconductor at="" r-project.org=""> >>> Subject: [BioC] edgeR: summary of differentially expressed genes or >>> tags >>> >>> Dear edgeR community, >>> >>> Good day. >>> >>> I can learn summary of the up and down regulated genes/tags from >>> >summary(de <- decideTestsDGE(lrt)) >>> when the *coef *of *glmLRT*(the likelihood ratio test) is set to one >>> degree >>> of freedom. >>> >>> When the *coef* is set to i.e. 2:5; the decideTestsDGE doesn't work. It >>> could be nice to see the summary of up and down regulated genes/tags when >>> the *coef* is set i.e. 2:5. >>> >>> Thus, may I ask is there any method to learn the number of up and down >>> regulated genes/tags when the *coef* of *glmLRT*(the likelihood ratio >>> test) is >>> set to all groups? >>> >>> Thank you very much for your guys time and help. >>> >>> Have a nice weekend. >>> >>> Best regards, >>> KJ Lim >>> >> >> >> ______________________________**______________________________**___ _______ >> The information in this email is confidential and intended solely for the >> addressee. >> You must not disclose, forward, print or use it without the permission of >> the sender. >> ______________________________**______________________________**___ _______ >> > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}