MCB/ABE/BIOC/ECOL/GENE 416A/516A

Statistical Bioinformatics and Genomic Analysis

Fall 2011

Time & location: TTh 11:00 am - 12:15 pm, Shantz 338

Instructor: Lingling An

Office: Shantz 501

Phone: (520) 621-1248

Email: anling@email.arizona.edu

Office hours: Thursday 10:00-11:00am or by appointment

Syllabus: here

Useful tools: R CRAN and reference card, Bioconductor.

textbook:

Announcement:

homework 4 solution

homework 5 solution

final exam: 1-3pm, Dec 14

Review for the final exam – Dec 6^th

Project report will be due on Dec 7th

Evaluation sheet for the project presentation

Instructions for the project

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Lectures and Homework assignments

(password is required for the files)

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Aug 23: Introduction (syllabus, survey)

Aug 25: Review (I): statistics (population & sample, parameter & statistic, normal and t- distributions,

central limit theorem, confidence intervals, two-sample comparison)

Aug 30: Review (II): statistics (hypothesis test, one-sided, two-sided tests, p-value and interpretation,

sample size, relationship between confidence interval and hypothesis test)

Sep 1: Review (III): statistics (ANOVA analysis, mean square error, F statistic, Least Significant

Difference test, multiple comparisons and Bonferroni correction)

Sep 6: Review: Intro to Molecular Biology

Sep 8: Introduction to R (example data is here)

Sep 13: Introduction to R graphics ,

homework 1 is here and the paper is here

homework 1 solution

Sep 15: Introduction to Microarray

Sep 20: Microarray Experiment

Sep 22: Data Preprocessing for cDNA array

Sep 27: Data Preprocessing for Affymetrix array

homework 2 is here , the dataset folder for the homework is here and the paper is here

manuals for packages of Affy and limma

homework 2 solution

Sep 29: Lab1 and R code

Oct 4: Differential expression analysis

Oct 6: Differential expression analysis (limma for affy data) (dataset for the lecture)

homework 3 is here , the dataset for the homework is here.

homework 3 solution

Oct 11: Differential expression analysis (limma for cDNA array data)

Oct 13: Review for the midterm

Oct 18: Introduction to cluster analysis

Oct 20: Midterm

Oct 25: Clustering gene expression

Oct 27: Cluster analysis (R code)

Nov 1: Classification analysis

Nov 3: Classification analysis (R code)

homework 4 is here and the paper is here

Nov 8: Lab 2

Nov 10: Gene Ontology analysis

Nov 15: Gene Ontology analysis (R code)

homework 5 is here and the paper is here

Nov 17: Pathway analysis

Nov 22: Lab 3 and gene list

Nov 27: Introduction to next generation sequencing technologies

Nov 29: Project presentations (I)

Dec 1: Project presentations (II)

Dec 6: Review for the final exam