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Affymetrix Microarray Tutorial
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UCLA Informatics Center for Neurogenetics and Neurogenomics (ICNN)
March 17, 2016
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390
Affymetrix Microarray Tutorial
Tutorial slides to accompany the GitHub Affymetrix Microarray Tutorial Page
UCLA Informatics Center for Neurogenetics and Neurogenomics (ICNN)
March 17, 2016
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Transcript
Affymetrix Microarray Tutorial Accompanying Slides UCLA ICNN
Overview 1. Get Data 2. QC on Non-Normalized Data 3.
Normalization 4. Batch Correction 5. Outlier Removal 6. QC on Normalized Data 7. Covariate Analysis 8. Annotating Probes 9. Collapse Rows 10. Differential Expression Analysis
1. Get Data datExpr Basic – Note that expression numbers
are not representative of real data in this example Probe Sample Sample 1 Sample 2 Etc… Probe A 3 4 Probe B 2 8 Etc….
1. Get Data datMeta Basic datMeta Example Sample Category Label
Gender Location Etc… Sample 1 Label A Male PreFrontal Cortex Sample 2 Label B Female Putamen Etc… Sample GSM Group Region N1A Normal-frontal GSM329660 CTL FCX N1C Normal-hippocampus GSM329661 CTL HPC N1B Normal-cerebellum GSM329662 CTL CBL
Overview 1. Get Data 2. QC on Non-Normalized Data 3.
Normalization 4. Batch Correction 5. Outlier Removal 6. QC on Normalized Data 7. Covariate Analysis 8. Annotating Probes 9. Collapse Rows 10. Differential Expression Analysis
2. QC on Non-Normalized Data
2. QC on Non-Normalized Data
2. QC on Non-Normalized Data MDS
Overview 1. Get Data 2. QC on Non-Normalized Data 3.
Normalization 4. Batch Correction 5. Outlier Removal 6. QC on Normalized Data 7. Covariate Analysis 8. Annotating Probes 9. Collapse Rows 10. Differential Expression Analysis
4. Batch Correction MDS Post-Normalization Pre-Batch Correction
4. Batch Correction MDS Post-Normalization Post-Batch Correction
4. Batch Correction MDS Post-Normalization Post-Batch Correction
Overview 1. Get Data 2. QC on Non-Normalized Data 3.
Normalization 4. Batch Correction 5. Outlier Removal 6. QC on Normalized Data 7. Covariate Analysis 8. Annotating Probes 9. Collapse Rows 10. Differential Expression Analysis
5. Outlier Removal
None
Overview 1. Get Data 2. QC on Non-Normalized Data 3.
Normalization 4. Batch Correction 5. Outlier Removal 6. QC on Normalized Data 7. Covariate Analysis 8. Annotating Probes 9. Collapse Rows 10. Differential Expression Analysis
6. QC on Normalized Data
6. QC on Normalized Data
6. QC on Normalized Data MDS
Overview 1. Get Data 2. QC on Non-Normalized Data 3.
Normalization 4. Batch Correction 5. Outlier Removal 6. QC on Normalized Data 7. Covariate Analysis 8. Annotating Probes 9. Collapse Rows 10. Differential Expression Analysis
7. Covariate Analysis
Overview 1. Get Data 2. QC on Non-Normalized Data 3.
Normalization 4. Batch Correction 5. Outlier Removal 6. QC on Normalized Data 7. Covariate Analysis 8. Annotating Probes 9. Collapse Rows 10. Differential Expression Analysis
8. Annotating Probes Probe Identifier Affy_probe Ensembl_ID Etc… 209_at 209_at
ENS00001 369_at 369_at ENS00345 Etc…. Example geneDat
Overview 1. Get Data 2. QC on Non-Normalized Data 3.
Normalization 4. Batch Correction 5. Outlier Removal 6. QC on Normalized Data 7. Covariate Analysis 8. Annotating Probes 9. Collapse Rows 10. Differential Expression Analysis
10. Differential Expression Analysis