[BioC] Differentially Expressed Genes in Time Series with Replications

[Peter Robinson]

Dear list,

I was wondering if anyone has some advice as to the best way of determining a list of DE genes for each time point of a series of experiments in which there are no replicates. (I am looking at the Spellman Yeast Cell Cycle data).

On the one hand I am familiar with some methods such as that by Storey et al (2005) "Significance analysis of time course microarray experiments" in PNAS, but these methods only tell me whether a gene is DE or not for the entire time course. I would like to have a list of such genes for each time point. I can think of several heuristics to make such a list, but I imagine there must be a better way of doing this.

Pointers within or without Bioconductor would be greatly appreciated.

Take care, Peter