[BioC] time course experiment

Gordon K Smyth smyth at wehi.EDU.AU
Wed Jul 23 01:03:47 CEST 2014


On Tue, 22 Jul 2014, Rao,Xiayu wrote:

> 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.

It's just convenience.  It can be done either way.

> 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

Actually there is no difference between the two from limma's point of 
view.  You simply compute any contrast of interest to you and then test 
for DE for that contrast.

> (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)

Actually, given the way you have computed your contrasts, you probably 
want to specify coef for any topTable.

Gordon

> 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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