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