Hi All,

Thank you Gordon and Richard very much.

In my data,for each time point i have the number of expressed genes and i
would like to find if the number of expressed genes at t1 is different from
number of  expressed genes at t2 ,or is different from all other time point
using statistical test.

the data look like this:

time                            t1  t2  .... tn
expressed genes        #  #   ......#

 I have only one group,Shall i use same design matrix ? shall i use df=5 as
in example??


Best Regards,
Chris

On Tue, Feb 5, 2013 at 12:02 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> Dear Rich,
>
> I have added a time course example using splines to the limma User's
> Guide, see page 48:
>
> http://bioconductor.org/**packages/2.12/bioc/vignettes/**
> limma/inst/doc/usersguide.pdf<http://bioconductor.org/packages/2.12/bioc/vignettes/limma/inst/doc/usersguide.pdf>
>
> Best wishes
> Gordon
>
> ------------------ original message ------------------
> [BioC] statistical test for time course data
> Richard Friedman friedman at cancercenter.columbia.edu
> Sun Feb 3 20:18:03 CET 2013
>
> Dear Gordon,
>
>         Thank you very much for the clarification. Now that I think of it,
> the one-against all is straightforward. However, If there are any worked
> examples you could point me towards for polynomial and spline modeling of
> the time series I would greatly appreciate it. I am especially interested
> in testing the hypothesis that the temporal behavior of 2 treatments are
> different.
>
> Best wishes,
> Rich
>
> ______________________________**______________________________**__________
> The information in this email is confidential and inte...{{dropped:13}}

