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@illinois.edu<mailto:drnevich@illinois.edu>


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