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) • 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)

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.)

Affymetrix QC Metrics Back to work flow

Principle Component Analysis Back to work flow

Intensity Histogram Back to work flow

ANOVA: Source of Variance Back to work flow

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

Unsupervised Hierarchical Clustering Back to work flow

Scatter plot Back to work flow

Gene Annotations Back to work flow

Gene Ontology: GATHER Back to work flow

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

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

Pathway Analysis: pathway Back to work flow

Pathway Analysis: network

Data Analysis: General Workflow & Analysis Options