Hello all, 

I am working on a Yeast2 Affymetrix project. 

The yeast received one drug treatment at 3 concentration (0, 0.5, 1) with 10 time points for each treatment, without replication in each combination. 

eg:

drug  time
0           0
0           6
0           12
...
0.5         0
0.5         6
0.5        12

... 
1           90

My target is to test what genes  significantly change for the drug treatment and at which time points. 

I am using limma package.


My question is how I should make the model.matrix. 

It seems that I can't use  ~ Drug*Time, that will result in no residual degrees of freedom. 

Under such condition, may I put Variable Time into the model? Or I have to do one linear regression (~Drug) for each time point, respectively. 

Or any other package will work this analysis better?

Thank you for any suggestion!  I am a newcomer for Bioconductor. 

-Hong













________________________________
From: Steve Lianoglou <mailinglist.honeypot@gmail.com>
To: Nitish Kumar Mishra <nitishimtech@gmail.com>
Cc: bioconductor@r-project.org
Sent: Monday, June 6, 2011 8:42 PM
Subject: Re: [BioC] Significance of variance

Hi,

It sounds like you are trying to look for differentially expressed
genes in your data.

Can you just go back and use the raw data that this "variance vector"
was calculated from and then use something more principled/sound like
limma?

-steve

On Mon, Jun 6, 2011 at 11:13 PM, Nitish Kumar Mishra
<nitishimtech@gmail.com> wrote:
> Hi All,
> I have single variance value for gene-expression of several genes (variance
> for several repeats of experiments), so in this way I have a single column
> (with 98,00 row) value of variance. Now I just want to check variance of
> which gene is statically significance.
>  eg;
>
> 1.2
> 0.9
> 1.6
> 1.5
> 0.07
> 1.03
> .
> .
> .
>
> In nutshell I was to calculate the different p-value for each single value.
> Can any one suggest how I can calculate the P-value for each value of column
> vector.
>
> Thanks in advanced.
> --
> Nitish Kumar Mishra
> 3104E, CBCB, Biomolecular Sciences Bldg #296
> University of Maryland, College Park, MD 20742
> Phone (Off): 301-405-8218
> Mobile No: 240-898-7311
> nitish@umiacs.umd.edu
> mishran@umd.edu
>
>        [[alternative HTML version deleted]]
>
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>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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