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@@ -1,6 +1,9 @@
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This is a series of example plots and tables from a combined
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RNA-seq/ChIP-seq study on differences between naive and memory T-cell
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-activation.
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+activation. You can view the (old and messy) code for these plots
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+[here][1].
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+
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+[1]: https://github.com/DarwinAwardWinner/cd4-histone-paper-code
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- [`p-value distributions.pdf`](p-value distributions.pdf) is a series
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of p-value histograms for each of the contrasts tested. A contrast
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@@ -19,6 +22,11 @@ activation.
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studied. This was used to determine the "promoter radius" for read
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counting. Notably, the three histone marks do not all have the same
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promoter radius.
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+- [`rnaseq-MDSPlots.pdf`](rnaseq-MDSPlots.pdf) shows a series of MDS
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+ plots (similar to PCA plots) before and after correction of a known
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+ batch effect. Note the implausible zigzag-shaped progression over
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+ time before correction, compared to the more plausible cyclic time
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+ progression after.
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- [`rnaseq-edgeR-vs-limma.pdf`](rnaseq-edgeR-vs-limma.pdf) and
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[`rnaseq-limma-weighted-vs-uw.pdf`](rnaseq-limma-weighted-vs-uw.pdf)
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show comparisons of p-values for all genes in each contrast of the
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@@ -27,3 +35,31 @@ activation.
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sample quality weights.
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- [`rnaseq-maplots-limma-sampleweights.pdf`](rnaseq-maplots-limma-sampleweights.pdf)
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shows the MA plot for each contrast of the RNA-seq data
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+
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+
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+There are also some plots from an in-progress analysis of the same
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+data based on sliding windows, rather than just analyzing promoter
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+regions. You can view the code for generating these plots [here][2].
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+
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+[2]: https://github.com/DarwinAwardWinner/CD4-csaw
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+
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+- [`CCF-plots.pdf`](CCF-plots.pdf) shows the cross-correlation
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+ functions of several different histone marks, at several different
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+ levels of smoothing. This plot is used to determine the fragment
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+ size.
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+- [`site-profile-plots.pdf`](site-profile-plots.pdf) shows plots of
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+ the relative coverage depth profiles around local coverage maxima.
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+ This plot is used to determine the footprint size of the protein
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+ being imunoprecipitated. Since this is histone mark data, the
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+ footprint size should match the size of a nucleosome, about 147 bp.
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+- [`H3K4me3-window-abundance-vs-peaks.pdf`](H3K4me3-window-abundance-vs-peaks.pdf)
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+ shows the association between peak overlap status and abundance for
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+ all windows in the genome. As expected, windows that overlap a
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+ called peak tend to have a higher abundance than other windows.
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+- [`H3K4me3 Selected Sample 10KB Bin MA Plots.pdf`](H3K4me3 Selected
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+ Sample 10KB Bin MA Plots.pdf) shows selected MA plots between
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+ samples demonstrating the effects of several different potential
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+ normalization methods.
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+- [`H3K4me3-normfactors.pdf`](H3K4me3-normfactors.pdf) shows the
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+ associations between normalization factor and experimental variables
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+ for several different normalization methods.
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