[BioC] Help needed on limma and differentially expressed genes

[Ng Stanley]

Hi,

The design model is attached to this email.

I am using limma to analyze a set of microarray, but face with the
difficulty on the design matrix and contrast matrix even after reading the
limma userguide carefully. Basically, I need to exclude the effects of empty
plasmid transfected into the cells. Then identify

1) differentially expressed genes at 8h and 16h induced by the
over-expression of P53 with respect to 0h,
2) those genes that are differentially expressed from 8h to 16h  induced by
the over-expression of P53.

The experiment assumes that Wild type at 8h and 16h are the same as at 0h,
due to cost limitations.

Please help.

Thanks
Stanley
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