---------- Forwarded message ----------
From: chris Jhon <cjhon217@gmail.com>
Date: Wed, Feb 13, 2013 at 9:23 PM
Subject: Re: [BioC] statistical test for time course data
To: Richard Friedman <friedman@cancercenter.columbia.edu>


Hi ;

Thank you Richard for help.
I have the data like this table

Time  number
0hr     #
6hr     #
24hr   #

i tried to follow the example as in userguide and as Richard suggested
me,but  have the following questions:
in user guide
***************
> lev <- c("wt.0hr","wt.6hr","wt.24hr","mu.0hr","mu.6hr","mu.24hr")
> f <- factor(targets$Target, levels=lev)
> design <- model.matrix(~0+f)
> colnames(design) <- lev
> fit <- lmFit(eset, design)
***************

Q1) what about est, in this stage i would like to test the statistical
significance between numbers showed in second column which represents the
number of expressed genes,SHALL I REPLACE ESET WITH MYDATA$number??

when i tried so i got the following error   ---  Error in rowMeans(y$exprs,
na.rm = TRUE) : 'x' must be numeric

Q2) Can anyone explain for methe meaning of (~0+f) in
design <- model.matrix(~0+f)

Q3) how to design different matrices for different conditions,can any one
send me a tutorial for this.

Thank you very much in advance.




On Wed, Feb 6, 2013 at 10:30 PM, Richard Friedman <
friedman@cancercenter.columbia.edu> wrote:

> Dear Chris,
>
> For the questions you are asking I recommend not using splines.
> For the comparison of  t1 vs t2 us a design matrix which makes every point
> a different
> time point and then do t2 vs t1, For t1 compared to all other points, I
> would
> label t1 A, and all other points B.
>
> If anyone on the list has a different opinion in the matter I would
> appreciate hearing from them.
>
> With hopes that this helps,
> Rich
>
>
>
> On Feb 5, 2013, at 10:09 AM, chris Jhon wrote:
>
> 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
>>
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