[BioC] time course experiment

[Rao,Xiayu]

Hi, Gordon

Thank you for letting me know. As Jim suggested, I would just include everything in one command as below to make it simple. I now understand that the difference between testing for changed gene over time (the trend) and testing for diff genes between two exact time points is 
(1) to make different contrasts and 
(2) to use topTableF(fit) to extract the gene list for the former and to use topTable(fit, coef=1 or any other number) for the later. (Correct me if I am wrong, thank you)

contrast <- makeContrasts("mu.0hr-wt.0hr", "mu.6hr-wt.6hr", "mu.24hr-wt.24hr","wt.6hr-wt.0hr", "wt.24hr-wt.6hr", "wt.24hr-wt.0hr","mu.6hr-mu.0hr", "mu.24hr-mu.6hr", "mu.24hr-mu.0hr",levels=design)

Thanks,
Xiayu



-----Original Message-----
From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] 
Sent: Tuesday, July 22, 2014 5:26 PM
To: Rao,Xiayu
Cc: Bioconductor mailing list
Subject: time course experiment

Dear Xiayu,

I don't quite see the problem.  It all seems straightforward.  All the contrasts you have proposed seem simple and sensible.  There is no need nor possible advantage in subsetting the data.

Best wishes
Gordon

PS. I haven't included you original post in my reply because there were so many non-standard characters imbedded in it.

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