Version Info | Introduction | Differential Expression Analysis | More complex model designs. | Co-expression Analysis | Functional Analysis - Expression Data | Functional Analysis - general | Obtaining Reports | Functional Analysis - special options for reports | Command-line Package Usage | Usage | 1. Command line scripts for differential expression analysis. | Non-canonical usage scenarios: | A. Differential expression corrected by extra factors | B. Genes co-expression analysis with WGCNA | C. Analysing pre-normalized data with WGCNA | D. Using a pre-calculated list of DEA genes | E. Multifactorial (2x2) analysis to look for interactions between factors and effects in distinct groups | F. Multifactorial nested (2x2xn and 2xnxn) analysis to look for interactions between factors and effects in distinct groups where the groups contain paired samples (e.g. the same patient/control before and after treatment) | 2. Command line scripts for functional enrichment analysis. | DEgenes Hunter functional enrichment examples of use

Introduction | Combining technical replicates | Dealing with undetermined values | Selection of most stable reference/housekeeping genes | Normalization by means of reference/housekeeping genes

Introduction | read.LC480 | read.qPCR | read.taqman | qPCRBatch