Hello, I've analyzed a time course expt (on affy chips) with limma where there is one effect besides time. I've got 2 lists of significant diff expressed genes (one for each coefficient), have removed absent genes, and was wondering what the best way to get out which genes are positively affected and negatively effected...better yet, is there a way to calculate the actual fold changes for these genes for the two groups? Thanks in advance, and sorry if this is somewhat opaque - I am not familiar with linear modeling (in case it wasn't totally obvious) ;) -ken

On 10/19/05 12:43 PM, "Ken Termiso" <jerk_alert at="" hotmail.com=""> wrote: > Hello, > > I've analyzed a time course expt (on affy chips) with limma where there is > one effect besides time. I've got 2 lists of significant diff expressed > genes (one for each coefficient), have removed absent genes, and was > wondering what the best way to get out which genes are positively affected > and negatively effected...better yet, is there a way to calculate the actual > fold changes for these genes for the two groups? The M-value in the topTable output is the log2 fold change, so you can filter based on that column to get at the genes that you like. Sean