Dear List,

I need help with the analysis of time series experiment. I have cDNA
microarray data produced with genepix.
Bacterial cells were induced for sporulation (3 biological replicates), RNA
was extracted from cells before induction and after 1,2,3 and 4 hours after
induction. RNA from uninduced cells was labeled with Cy3, from respective
induced cells with Cy5 and hybriduzed onto two-color microarray.
To summarize the data:
# biol repl     Cy5    Cy3
3                 1h       unind
3                 2h       unind
3                 3h       unind
3                 4h       unind


How should I analyze this data to find differentially expressed genes?
I am trying to use limma package, but I cannot come up with proper design
matrix  to fit the linear model.


I will very much appreciate any help, as I am not very experienced
microarray data analyst.


Thank to everyone,
Olga.

	[[alternative HTML version deleted]]

