[BioC] Limma time course analysis : determining positively and negatively reg genes

[Ken Termiso]

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