Affymetrix Microarray Data Analysis - Concepts, Methods, and R functions Affymetrix Microarray Data CEL files: contain processed 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
Microarray Experimental Designs Biological and Technical Replicates Pooling, Blocking, Sample size determination the RNAs average out when pooled (biological averaging) 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 Histograms Images, residual images Boxplots RNA degradation plots