Dear Sam, Yes, you can test any comparison. > Date: Sun, 11 May 2014 20:53:41 -0400 > From: somnath bandyopadhyay <genome1976 at="" hotmail.com=""> > Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Subject: [BioC] limma all by all > > Hi, > I have microarray data from 10 different cell types. I want to identify > DEGs by an all cell type by all cell type comparison Perhaps just do an F-test. There are examples of this in the limma User's Guide. > and one cell type vs. all cell type comparison using limma. Just compute the contrast of one cell type versus the average of the rest. This is usually done with makeContrast() and contrast.fit(). Gordon > Is there a way to do it? > Thanks,Sam. ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}

Thanks Gordon! I will give it a try. Sam. > Date: Tue, 13 May 2014 17:32:59 +1000 > From: smyth@wehi.EDU.AU > To: genome1976@hotmail.com > CC: bioconductor@r-project.org > Subject: limma all by all > > Dear Sam, > > Yes, you can test any comparison. > > > Date: Sun, 11 May 2014 20:53:41 -0400 > > From: somnath bandyopadhyay <genome1976@hotmail.com> > > Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> > > Subject: [BioC] limma all by all > > > > Hi, > > > I have microarray data from 10 different cell types. I want to identify > > DEGs by an all cell type by all cell type comparison > > Perhaps just do an F-test. There are examples of this in the limma User's > Guide. > > > and one cell type vs. all cell type comparison using limma. > > Just compute the contrast of one cell type versus the average of the rest. > This is usually done with makeContrast() and contrast.fit(). > > Gordon > > > > Is there a way to do it? > > Thanks,Sam. > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:9}}