====== Quality Control of Gene Expression Data ======

===== Introduction =====

High-throughput gene expression platforms are powerful techniques but are quite susceptible to variations, either be from biological or technical sources. This is a non-exhaustive list of possible variation sources:

=== Biological Variability ===

  * Genetic variations
  * Biomaterial sampling
  * Quality/quantity of the extracted mRNA

=== Technical Variability ===

  * mRNA processing (i.e.: cDNA synthesis)
  * Fluorophore incorporation
  * Array quality
  * Hybridization
  * Image acquisition

Because of this, it is best to verify before hand the quality of the data before getting into the normalization/summeraization process and the following analysis process. Replicates showing excessive variations will induce problems afterward, creating excessive noise in the data.

===== Mechanically-spotted arrays: quality control =====

==== GUI methods ====

  * More to come: using SpotFinder

==== CLI methods ====

  * [[.:2colors_aqm|arrayQualityMetrics()]]

===== Affymetrix: Quality Control =====

==== GUI Methods ====

  * More to come: using RMAExpress to get NUSE and RLE graphs
==== CLI methods ====

  * [[.:affy_simpleaffy|affy() and simpleaffy()]]
  * [[.:affy_affyqcreport|affyQCReport()]]
  * [[.:affy_affyplm_qc|affyPLM()]]
  * [[.:affy_aqm_affy|arrayQualityMetrics()]]

===== Illumina: Quality Control =====

  * More to come...

==== CLI methods ====

  * [[.:illumina_aqm|arrayQualityMetrics()]]
  * [[.:illumina_lumi|lumi()]]