[BioC] small mistake in edgeRUsersGuide()

Gordon K Smyth smyth at wehi.EDU.AU
Wed Jul 16 00:51:06 CEST 2014


Hi Jenny,

You're right, fit should be redefined in Section 3.2.5 for the reference 
in Section 3.2.6 to make sense.  Thanks for pointing this out.  Now fixed.

Best wishes
Gordon

---------------------------------------------
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
http://www.statsci.org/smyth

On Tue, 15 Jul 2014, Zadeh, Jenny Drnevich wrote:

> Hello,
>
> I found a small mistake in the edgeRUsersGuide (revised 17 June 2014) in 
> section 3.2.5, an omission in the sample code. On page 24 the example 
> creates the object "fit" using a design matrix that has a column for 
> each group. On page 26 in section 3.2.5 it shows switching the design 
> matrix to one with an intercept term, but the example doesn't show 
> recreating the "fit" object. This is the omission. It does show making a 
> "design2" and "fit2" objects using re-leveled groups. Then in section 
> 3.2.6 it says "with fit as above" and shows how to calculate a oneway 
> ANOVA. I had originally read 3.2.6 first, then went back to find how 
> "fit" was created and was confused at first because the last place "fit" 
> was created was with the wrong design matrix for calculating an anova 
> using coef=2:3. I was able to figure it out pretty quickly, but I 
> thought I would point it out.
>
> Thanks,
> Jenny
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> High Performance Biological Computing Program
> and The Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
> NOTE NEW OFFICE LOCATION
> 2112 IGB
> 1206 W. Gregory Dr.
> Urbana, IL 61801
> USA
> ph: 217-300-6543
> fax: 217-265-5066
> e-mail: drnevich at illinois.edu<mailto:drnevich at illinois.edu>
>
>

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