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Bugfix in the calculation of GSVA scores when abs.ranking=TRUE and kernel=FALSE.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSVA@129456 bc3139a8-67e5-0310-9ffc-ced21a209358

Robert Castelo authored on 08/05/2017 12:17:04
Showing 2 changed files

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@@ -1,5 +1,5 @@
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 Package: GSVA
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-Version: 1.25.0
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+Version: 1.25.1
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"))
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@@ -72,8 +72,7 @@ void row_d(double* x, double* y, double* r, int size_density_n, int size_test_n,
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 			left_tail += rnaseq ? ppois(y[j], x[i]+bw, TRUE, FALSE) : precomputedCdf(y[j]-x[i], bw);
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 		}
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 		left_tail = left_tail / size_density_n;
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-		/* r[j] = -1.0 * log((1.0-left_tail)/left_tail); */ /* log-odds not necessary */
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-    r[j] = left_tail;
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+		r[j] = -1.0 * log((1.0-left_tail)/left_tail);
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 	}
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 }
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