Hello Bioc members, I got a question about using limma to extract up-regulated genes from Affymetrix microarray datasets. I have created a design matrix, called lmfit, make the contrasts, call eBayes. But now I am stuck on what to do next. I check out the topTable function, but it only allows me to select differentially expressed genes. I am only interested in the up-regulated genes. How would I go about extracting only the up-regulated gnes? Thank you! Sincerely, Victoria [[alternative HTML version deleted]]

On Sat, Sep 25, 2010 at 4:13 PM, Victoria Hu <isabella_2726@hotmail.com>wrote: > > > > > Hello Bioc members, > > I got a question about using limma to extract up-regulated genes > from Affymetrix microarray datasets. > > I have created a design matrix, called lmfit, make the contrasts, call > eBayes. But now I am stuck on what to do next. I check out the topTable > function, but it only allows me to select differentially expressed > genes. I am only interested in the up-regulated genes. How would I go > about extracting only the up-regulated gnes? > > > Hi, Victoria. Look at the logFC or t columns? These will be positive for upregulated genes. You might want to look at the sort.by and resort.by arguments to topTable, also. Sean [[alternative HTML version deleted]]