Welcome to the web-site for
Bioinformatics II
        (Spring 2003)

Meetings: Tue, Thur 2.30-3.45pm, 124 Ag Eg

Francesca Chiaromonte
411 Thomas Bldg, 5-7075, chiaro@stat.psu.edu
Off. Hours: Wed 12.00-1.00pm, Thur 10.00-11.00am
Webb Miller
326A Pond Lab, 5-4551, webb@cse.psu.edu


Special announcements

1. Introduction to Microarrays

Notes, general introduction and spotted arrays

Affymetrix arrays:

Replicating: Reading List

Reading assignment: Naef F./Magnasco M. et al. (2001), From features to expression: high density oligonucleotide arrays analysis revisited. Write a summary and your comments in 2 pages (max), to hand in on Thur Jan 30th (in class).

2. Preprocessing of Microarray data I: Normalization and Missing Values


An instance of "global" normalization:

An instance of "control-based" normalization: Missing values: Reading List

Reading assignment: (this concerns both module 2 and 3) Tsodikov A., Szabo A., Jones D. (2002). Adjustments and measures of differential expression for microarray data. Bioinformatics 18(2), 251-260 (article). Write a summary and your comments in 4 pages (max), to hand in on Thur Mar 6th (in class). Work in groups.

3. Preprocessing of Microarray data II: Filtering, differentially expressed genes, other Transformations


Reading List

4. Dimension reduction and microarray data

Notes A
Notes B
Notes C

Reading List

5. Clustering and microarray data

Notes A
Notes B
Notes C

Reading List

Data analysis assignment: (this concerns both module 4 and 5). Hand in on Tue Apr 22 (in class). Work in groups. Instructions. Data (Excell file).
Data analysis assignment: (for final discussion on Thur May 1). Working in groups, do one of the following
(a) Perform a perturbation analysis to select an appropriate number of clusters (e.g. along the lines proposed by Ben-Hur et al.) for
the Yeast Shock data - previous assignment.
(b) Perform an analysis of your choice (chose the data, preprocess if needed, perform selection of differentially expressed genes,
dimension reduction, clustering, depending on the question you are trying to address).

Relevant Links