resume/examples/Salomon/CD4/README.mkdn

This is a series of example plots and tables from a combined
RNA-seq/ChIP-seq study on differences between naive and memory T-cell
activation.

- [p-value distributions.pdf](p-value distributions.pdf) is a series
  of p-value histograms for each of the contrasts tested. A contrast
  with no significant differential expression would exhibit a uniform
  distribution, while differential expression would be reflected by an
  excess of small p-values.
- [FPKM by Peak Status H3K4.pdf](FPKM by Peak Status H3K4.pdf) shows
  the variation in gene expression based on the presence or absence of
  two histone marks in the gene promoters.
- [promoter-edger-topgenes3-ql.xlsx](promoter-edger-topgenes3-ql.xlsx)
  is a spreadsheet of all promoters with differential histone
  modification in their promoters based on the ChIP-seq read counts.
- [Promoter Peak Distance Profile.pdf](Promoter Peak Distance Profile.pdf)
  shows the distribution of distances from transcription
  start sites to the nearest peak for the three histone modifications
  studied. This was used to determine the "promoter radius" for read
  counting. Notably, the three histone marks do not all have the same
  promoter radius.
- [rnaseq-edgeR-vs-limma.pdf](rnaseq-edgeR-vs-limma.pdf) and
  [rnaseq-limma-weighted-vs-uw.pdf](rnaseq-limma-weighted-vs-uw.pdf)
  show comparisons of p-values for all genes in each contrast of the
  RNA-seq data, comparing edgeR and limma-voom with/without sample
  quality weights. The final choice of method was limma-voom with
  sample quality weights.
- [rnaseq-maplots-limma-sampleweights.pdf](rnaseq-maplots-limma-sampleweights.pdf)
  shows the MA plot for each contrast of the RNA-seq data