[BioC] LIMMA vs. dChip

[jun.yan.a at utoronto.ca]

Dear list member,
I have a set of Affymetrix data of 10 arrays, HG_U133A, seperated into unpaired 
two groups of 5 arrays each. I processed the data using LIMMA and dChip. For 
dChip, I used all the default setting. The resulted differential expressed 
genes of the two have only less than 50% in common.

Why the number of the overlapped genes of the two results is so low? Is there 
any problems? Can anyone help me?

Thanks in advance,
Jun