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- # Human globin protocol stats
- This is a pair of spreadsheets summarizing the globin-reducing
- properties of an experimental RNA-seq protocol.
- - [method-select.xlsx](method-select.xlsx) shows the results for
- several different methods of globin reduction. The most important
- column is "Non-HB", which represents the fraction of total reads
- that map to non-globin genes.
- - [concentration-select.xlsx](concentration-select.xlsx) shows the
- results of selecting the best globin blocking method and optimizing
- the concentration of blockers as well as the number of
- hybridizations.
- # Cyno globin plots
- This is a series of example plots for evaluation of a similar globin
- reduction protocol that was designed for cynomolgus monkeys.
- - [BCVplots.pdf](BCVplots.pdf) and [corrplot.pdf](corrplot.pdf) show,
- respectively, that the biological coefficient of variation is not
- increased, and the sample-to-sample correlation is not decreased, by
- the globin reduction protocol.
- - [cyno-vs-hg19.pdf](cyno-vs-hg19.pdf) shows excellent correlation
- between total read counts on the cyno and human genomes, indicating
- 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
- between p-values from edgeR, limma-voom, and DESeq2 on the exact
- same differential expression test. Surprisingly, despite the
- significant algorithmic differences, edgeR and limma are in quite
- close agreement. DESeq2 id overly liberal because it does not
- account for the negative estimation bias in negative-binomial
- dispersions.
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