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Data Analysis: General Workflow & Analysis Options

Data Analysis: General Workflow & Analysis Options. Duke Microarray Core Facility Zhengzheng Wei July. 2011. Overall Workflow. Normalization (RMA, MAS5) Outlier Sample Removal ( Affymetrix QC matrics , PCA , intensity histogram )

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Data Analysis: General Workflow & Analysis Options

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  1. Data Analysis: General Workflow & Analysis Options Duke Microarray Core Facility Zhengzheng Wei July. 2011

  2. Overall Workflow • Normalization (RMA, MAS5) • Outlier Sample Removal (Affymetrix QC matrics, PCA, intensity histogram) • Gene Selection (ANOVA, multiway ANOVA, paired t-test, Fold Change…) • Gene annotations • Venn Diagram for Genelists • Clustering (unsupervised hierarchical clustering) • Gene Ontology Analysis (GATHER, Partek GO Enrichment, DAVID) • Pathway Analysis (MetaCore, DAVID, KEGG Pathways)

  3. Other Analysis Options • microRNA microarray data analysis • Exon array data analysis • Integrate microRNA data with mRNA expression data • Class prediction (K-Nearest Neighbor, support vector machine etc.) • Survival analysis • Power analysis • Chromosome view of expression data • Data filtering based on expression • Data transformations (impute missing data, scaling, quantile normalization, normalize to control, log transformation, normalize to baseline, loess, batch effect removal etc.)

  4. Affymetrix QC Metrics Back to work flow

  5. Principle Component Analysis Back to work flow

  6. Intensity Histogram Back to work flow

  7. ANOVA: Source of Variance Back to work flow

  8. Venn Diagram: Union and intersection of Genelists Back to work flow

  9. Unsupervised Hierarchical Clustering Back to work flow

  10. Scatter plot Back to work flow

  11. Gene Annotations Back to work flow

  12. Gene Ontology: GATHER Back to work flow

  13. Gene Ontology: Table with Enrichment score Back to work flow Next

  14. Gene Ontology: Bar & Pie & forest Chart Back to work flow

  15. Pathway Analysis: pathway Back to work flow

  16. Pathway Analysis: network

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