Dear Prof. Smyth, Thank you for the reply. I am really very sorry for asking new question in the this thread. Next time I will Keep this in mind. Kind Regards On Fri, Jan 3, 2014 at 4:05 AM, Gordon K Smyth <smyth@wehi.edu.au> wrote: > 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@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 intended solely for the >>> addressee. >>> You must not disclose, forward, print or use it without the permission of >>> the sender. >>> ______________________________________________________________________ >>> >>> >> >> >> -- >> 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}}