Ryan C. Thompson
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|---|---|---|
| .. | ||
| BCVplots.pdf | vor 9 Jahren | |
| README.mkdn | vor 9 Jahren | |
| concentration-select.xlsx | vor 9 Jahren | |
| corrplot.pdf | vor 9 Jahren | |
| cyno-vs-hg19.pdf | vor 9 Jahren | |
| maplot.pdf | vor 9 Jahren | |
| method-select.xlsx | vor 9 Jahren | |
| pval-comparisons.pdf | vor 9 Jahren | |
README.mkdn
# 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.
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.