Lawrence Hunter, Ph.D. Director, Computational Bioscience Program University of Colorado School of Medicine Microarrays Tzu Lip Phang, Ph.D. Associate Professor of Bioinformatics Division of Pulmonary Sciences and Critical Care Medicine University of Colorado School of Medicine

Data Science AKA BIG DATA

The Devils is in the Details

Workshop

The Central Dogma Transcriptome Genome

Microarrys in the Literature

Microarray: Primer

Basic Statistical Analysis

Power Analysis How many biological replication? My experience; at least 3, preferably 5, even 7 Bioconductor: SSPA

Basic Statistical Analysis

QC Including image analysis, normalization, and data transformation Data normalization: – Remove systematic errors introduced in labeling, hybridization and scanning procedures – Correct these errors while preserve biological variability / information

Why normalization?

To normalize or not to …

Basic Statistical Analysis

Statistical Testing Hypothesis Testing: Is the means of two groups different from each other – Fold Change – Student-T Test

Student-T Test

What is Multiple Comparison Testing??! GenesP-values Critical levelHo Gene <=0.051 Gene <=0.051 Gene <=0.051 Gene <=0.051 Gene <=0.051 Gene 60.09<=0.050 Gene 70.05<=0.050 Gene 80.09<=0.050 Gene 90.2<=0.050 Gene 100.3<=0.050 Alpha level = 0.05

When large number of tests … GenesP-values Critical levelHo Gene <=0.051 Gene <=0.051 Gene <=0.051 Gene <=0.051 Gene <=0.051 Gene 60.09<=0.050 …………… …………… Gene <=0.050 Gene <=0.050 Alpha level = wrong genes …

Correction … Bonferroni GenesP-values Critical levelHo Gene <= Gene <= Gene <= Gene <= Gene <= Gene 60.09<= ……… … ……… … Gene <= Gene <= Alpha level = 0.05 / 1000 =

Strike the balance … BonferroniNo correction False Discovery Rate Most ConservativeMost Lenient The False Discovery Rate (FDR) of a set of predictions is the expected percent of false predictions in the set of predictions. Example: If the algorithm returns 100 genes with false discovery rate of 0.3, then we should expect 70 of them to be correct

Put them together

Basic Statistical Analysis

Biological Interpretation