Dear Prof. Smyth,

Thankyou very much for the clasrification.

Though, I would like to ask one more question regarding EdgeR. I want to
known How to extract the normalized count using EdgeR?. I search though
internet and found a reply by Mark (
https://stat.ethz.ch/pipermail/bioconductor/2012-July/046795.html) to use
cpm for this purpose, Whereas some also suggest using pseudocount(
http://www.biostars.org/p/54817/) and normalized value on lo2 scale(
https://stat.ethz.ch/pipermail/bioconductor/2012-March/044311.html). I
understand the cpm and log2 based normalizaed count, but couldn't exactly
get the concept of pseudocount.

So for extracting normalized count shall I go for cpm?

Kind Regards




On Thu, Jan 2, 2014 at 3:33 AM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> Dear Reema,
>
> Yes, you can use the glm based analysis for two groups.  The results will
> be similar to using the exact test, but the p-values will be based on an
> asymptotic approximation rather than being exact.
>
> Best wishes
> Gordon
>
>  Date: Tue, 31 Dec 2013 20:47:31 +0000
>> From: Reema Singh <reema28sep@gmail.com>
>> To: bioconductor <bioconductor@r-project.org>,  Bioconductor mailing
>>         list <bioconductor@stat.math.ethz.ch>
>> Subject: [BioC] EdgeR glm based analysis
>>
>> Dear All,
>>
>> First, wish you all a very happy and prosporous New Year.
>>
>> In EdgeR manual[Case Studies section], for two group comparison, generally
>> exactTest usage is shown, whereas for the multiple group comparison glm
>> based analysis has been shown. In 1.4 quick start section, use of glm
>> based
>> analysis for two group comparison is mentioned with an additional use of
>> design matrix.
>>
>> Now my question :- Is it ok to use glm based analysis for two group
>> comparison? I would appreciate any suggestion.
>>
>>
>> Kind Regards
>>
>>
>> --
>> Reema Singh
>> Postdoctoral Research Assistant
>> College of Life Sciences
>> University of Dundee,
>> Dundee DD1 4HN, Scotland
>> United Kingdom
>>
>
> ______________________________________________________________________
> The information in this email is confidential and inte...{{dropped:20}}

