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| 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 |
#acl All:read = 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 |
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