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Add figures from latest version of globin paper

Ryan C. Thompson 9 years ago
parent
commit
e3eb9a56f6

+ 16 - 3
examples/Salomon/globin/README.mkdn

@@ -24,9 +24,6 @@ reduction protocol that was designed for cynomolgus monkeys.
 - [`cyno-vs-hg19.pdf`](cyno-vs-hg19.pdf) shows excellent correlation
 - [`cyno-vs-hg19.pdf`](cyno-vs-hg19.pdf) shows excellent correlation
   between total read counts on the cyno and human genomes, indicating
   between total read counts on the cyno and human genomes, indicating
   that the cyno annotation is reasonably complete.
   that the cyno annotation is reasonably complete.
-- [`maplot.pdf`](maplot.pdf) shows an MA plot of the effects of globin
-  reduction. Notably, there are real and significant effects on
-  non-globin genes, but they are consistent and predictable.
 - [`pval-comparisons.pdf`](pval-comparisons.pdf) shows the comparison
 - [`pval-comparisons.pdf`](pval-comparisons.pdf) shows the comparison
   between p-values from edgeR, limma-voom, and DESeq2 on the exact
   between p-values from edgeR, limma-voom, and DESeq2 on the exact
   same differential expression test. Surprisingly, despite the
   same differential expression test. Surprisingly, despite the
@@ -34,3 +31,19 @@ reduction protocol that was designed for cynomolgus monkeys.
   close agreement. DESeq2 id overly liberal because it does not
   close agreement. DESeq2 id overly liberal because it does not
   account for the negative estimation bias in negative-binomial
   account for the negative estimation bias in negative-binomial
   dispersions.
   dispersions.
+
+# Publication plots
+
+These are the figures from an upcoming publication on the developed
+globin blocking method.
+
+- [Figure 1](figure1 - globin-fractions.pdf): Globin blocking (GB)
+  substantially increases yield and consistency of non-globin reads.
+- [Figure 2](figure2 - aveLogCPM-colored.pdf): GB lowers the noise
+  floor and increases the distance between noise floor and signal.
+- [Figrue 3](figure3 - detection.pdf): GB allows detection of more
+  genes at any abundance threshold.
+- [Figure 4](figure4 - maplot-colored.pdf): GB has small but
+  systematic effects on other genes' measured expression levels.
+- [Figure 5](figure5 - corrplot.pdf): GB Significantly increases
+  correlation between libraries.

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examples/Salomon/globin/figure1 - globin-fractions.pdf


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examples/Salomon/globin/figure2 - aveLogCPM-colored.pdf


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examples/Salomon/globin/figure3 - detection.pdf


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examples/Salomon/globin/figure4 - maplot-colored.pdf


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examples/Salomon/globin/figure5 - corrplot.pdf