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= Summary of Affymetrix Microarray Data Analysis =

1. Affymetrix Microarray Data 
 * CEL files: contain intensity values, higher intensity (transcript abundance) more active genes
 * CDF (chip description file) files: specify the probe and probe set to which each cell belongs
 * Terms:
   * Probe: oligonucleotides of 25 base (pair) length used to probe RNA targets (25 base sequence)
   * Probe pair: a unit composed of a perfect match (PM) and its mismatch (MM)
   * Probe pair set: PMs and MMs related to a common affyID (a group of probe pairs corresponds to a particular gene or a fraction of a gene. Some genes are represented by more than one probe set.)
   * affyID: an identification for a probe set (which can be a gene or a fraction of a gene) represented on the array

2. Microarray Experimental Designs 
 * Biological and technical replicates
 * Pooling (biological averaging), blocking
 * Sample size determination

3. Data Exploration 
 * MA plots
   * M values are log fold changes, M=log2(T/C)=log2(T)-log2(C)
   * A values are average log intensities between two arrays, A=(log2(T)+log2(C))/2
 * Images, residual images
 * Histograms, boxplots
 * RNA degradation plots