[BioC] looking for advice on analysis methods

[David Horvath]

Hi all,

I am new to this field, and am looking for advice on what analysis methods I should use. I have used microarray in an attempt to identify changes in gene expression in buds over time. My comparison scheme was time=X1 Cy3 vs  control Cy5, Time=X3 Cy5 vs control Cy3: (X1=aug01, sep01, oct01, nov01, dec01) (X3=aug03, sep03, oct03, nov03, dec03). I have downloaded R and LIMMA and have managed (with help) to remove low intensity and bad spots, perform a print-tip loess normalization of the data for each hybridization, and get the normalized ratios. However, the next step to figure out which genes are significantly differentially expressed  has me confused (lots of possibilities, and I am not a statistician).  Any assistance on which analysis commands or techniques would be greatly appreciated.

Thanks!

Dave Horvath
USDA/ARS