edgeR: a Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data
Bioinformatics, 2009 · paper · Biomedicine
Describes edgeR, a Bioconductor software package for testing differential expression in replicated count data. It uses an overdispersed Poisson model with empirical Bayes moderation, and works even with minimal replication.
Checked: PDF from europepmc.org, fetched 4 Oct 2026. Page numbers are those of that PDF.
2 findings
Reference or label References, Smyth (2004): "Stat. Appl. Genet. Mol. Biol., 1, Art 3." — the bold volume position holds "1"; the article is reportedly in volume 3 (issue 1, Article 3).
- p. 2 References, Smyth,G.K. (2004)
Stat. Appl. Genet. Mol. Biol., 1, Art 3.
- p. 2 References, Smyth,G.K. (2004)
1, Art 3.
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: that Smyth (2004) appeared in Statistical Applications in Genetics and Molecular Biology volume 3, issue 1, Article 3, and that the journal's volume 1 was 2002. The crop shows bold "1" followed by "Art 3" in the position where every other entry prints the volume in bold (e.g. "Bioinformatics, 23, 2881–2887"). The printed text is as quoted; the true volume cannot be checked from the files.
Second check: another model agreed
Report a problem with this finding
Wording Section 2: "In general, φg represents the coefficient of variation of biological variation between the samples" — with the stated variance "µgi(1+µgiφg)", φg is the squared coefficient of variation; the CV is sqrt(φg).
- p. 1 Section 2 Model, last paragraph
In general, φg represents the coefficient of variation of biological variation between the samples
- p. 1 Section 2 Model, after Eq. (1)
µgi(1+µgiφg)
- p. 1 Section 2 Model, last paragraph
In general, φg represents the coefficient of variation of biological
Judge's note: Read the page 1 image and crop: the variance is printed as µgi(1+µgiφg) = µ + φµ², and the sentence has no "squared" or superscript. The extra-Poisson variance is φµ², so its SD is µ·sqrt(φ) and the biological CV is sqrt(φ), making φ = CV². Nothing in the two pages defines φ differently. Rated S3 because the equation itself is correct and only the verbal description is off by a square.
Second check: another model agreed
Report a problem with this finding
2 minor (typos and the like; most checked by the judge only)
Typo Misspelling in Introduction para 2 (p.1): "is an implementation of methology developed by Robinson and Smyth (2007, 2008)" — should read "methodology".
- p. 1 Section 1 Introduction, second paragraph
of methology developed by Robinson and Smyth (2007, 2008)
- p. 1 Introduction, para 2
implementation of methology developed by Robinson and Smyth
- p. 1 Section 1 Introduction, right column, second paragraph
is an implementation of methology developed by Robinson and Smyth (2007, 2008)
- p. 1 Introduction, 2nd paragraph
an implementation of methology developed by Robinson and Smyth (2007, 2008)
Judge's note: In the crop of PDF page 1, the typeset text reads "of methology developed by Robinson and Smyth (2007, 2008)." The word sits whole on one line with no hyphenation, so it is not an extraction artefact. The paper spells the word correctly elsewhere: "The methodology can be used" in the abstract and "The initial methodology worked only" in the main text. The fix is to change it to "methodology".
Second check: none (judge only)
Report a problem with this finding
Typo References: "Smyth,G.K. and Verbyla,A.P. (1996). A conditional approach" — stray full stop after the year; every other entry has no punctuation after the year, e.g. "Smyth,G.K. (2004) Linear models".
- p. 2 References, Smyth and Verbyla
Smyth,G.K. and Verbyla,A.P. (1996). A conditional approach
Judge's note: The crop and page 2 image show the full stop after "(1996)" in this entry only. The other eight entries run from the year straight into the title. Cosmetic.
Second check: none (judge only)