Chapter 3 Exploring and visualising biomolecular data

This chapter provides an overview of a typical omics data analysis, exploration of the data, statistical analysis and their associated visualisations. We will look into the respective figures and how to produce them in the later chapters.

A typical proteomics data processing and analysis workflow

Raw data

Tracking an ion from the chromatogram to the MS2 spectra

See here for details and code.

Raw data QC

See ?plotMzDelta for details and code.

Exploring the experimental design

table(cut(crc$Age, 5), crc$Gender)

##              
##               female male
##   (32.9,44.6]      3    2
##   (44.6,56.2]     19   14
##   (56.2,67.8]     34   59
##   (67.8,79.4]     28   28
##   (79.4,91.1]     10    3

## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

Quantitative data

Differential expression