[BioC] EdgeR glm based analysis

[Gordon K Smyth]

See sections 2.5 (Normalization) and 2.10 of the edgeR User's Guide.

Gordon

PS. If you ask a new question, better to start a new thread with a new 
subject.

On Thu, 2 Jan 2014, Reema Singh wrote:

> 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 at 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 at gmail.com>
>>> To: bioconductor <bioconductor at r-project.org>,  Bioconductor mailing
>>>         list <bioconductor at 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 intended solely for the
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>> ______________________________________________________________________
>>
>
>
>
> -- 
> Reema Singh
> Postdoctoral Research Assistant
> College of Life Sciences
> University of Dundee,
> Dundee DD1 4HN, Scotland
> United Kingdom
>

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