Entering edit mode
chris Jhon
▴
260
@chris-jhon-5047
Last seen 10.3 years ago
---------- 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
>>
>> ______________________________**______________________________**
>> __________
>> The information in this email is confidential and
intend...{{dropped:4}}
>>
>> ______________________________**_________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor="">
>> Search the archives: http://news.gmane.org/gmane.**
>> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor="">
>>
>
>
>
[[alternative HTML version deleted]]