[BioC] statistical test for time course data

[Richard Friedman]

On Feb 13, 2013, at 7:24 AM, chris Jhon wrote:

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

Chris,

> 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

It does not express the number of genes. eset contains the expression data,


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

I myself am vague on this point, but typing 

design

will give you your design matrix.


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


In the targets file label all of the time points except the one to be left out as a.
Label the others b.

You can send me your targets file when you do this (send to the list as well).

With hopes that this helps,
Roc

> Thank you very much in advance.
> 
> 
> 
> 
> On Wed, Feb 6, 2013 at 10:30 PM, Richard Friedman <
> friedman at 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 at 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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>> 
>> 
>> 
> 
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