BIOSTATISTICS 140.688: STATISTICS FOR GENE EXPRESSION, Spring 2001
Monday and Wednesday from 10:30 to 12
School of Hygiene and Public Health, room W3204

This course will be taught again in the 4th term of 2002, at the same times, and probably the same location. Stay tuned.


The course syllabus for spring 2002 will be somewhat revised,
more emphasis will be placed on Affy probe level analysis, normalization, and identification of differntial gene expression.
There will be a small midterm project and a final, based on the same data set for all students.
Some of the Software packages listed in this link will be discussed in detail.


Follow this Link to download R
GOALS

The goals of the class are to introduce statistical concepts and tools necessary to interpret and critically evaluate the literature on gene expression array data, and to survey open statistical challenges in the analysis of gene expression. The format is a hybrid between a journal club and a traditional class. The list of articles includes some of the most prominent array analyses from the biological and medical literature, as well as a selection of papers from the statistics and computer science literature. Advanced statistical material will be presented at an intuitive level. However, knowledge of basic probability and familiarity with regression are a prerequisite.


COURSE SYLLABUS AND MATERIALS

Please click on the painting to access the detailed syllabus and course materials.

A detail from Paul Cézanne's "Pommes et biscuits" (normal and overexpressed apples), 1879-1882 from the Musée de l'Orangerie, Paris. Cézanne was a precursor of expressionism in more ways than it is sometimes realized....



MATCHMAKING

Thanks to all students who sent their information. Here are the lists for possible matchmaking:
Closer to biology: Liying Zhang lzhang@jhsph.edu, Xiao Liu xiaoliu@mail.jhmi.edu, Thomas Cappola tcappola@jhmi.edu, Arne IJpma arne@mail.jhmi.edu
Closer to stats: Fang-Chi Hsu fhsu@jhsph.edu, Dongmei Liu , Zhijin Wu zwu@jhsph.edu, Hongling Zhou hzhou@jhsph.edu
Somewhere in between: Patty Gravitt gravittp@mail.nih.gov
plus some others as yet unclassified....


TOPICS

The syllabus is a broad overview of all steps of microarray data production, management and analysis, with deeper digressions into clustering, classification, and statistical pattern recognition. Topics include:
  • Background on gene expression
  • Expression array technologies
  • Basic array bioinformatics
  • Algorithms for image analysis
  • Normalization and bias adjustments; floor and ceiling effects
  • Estimating ratios: the small denominator trap
  • Importance of replication
  • Clustering
  • Selecting of genes for further study
  • Dimension reduction and orthogonalization; SVD; Principal components.
  • Binary regression
  • Recursive partitioning; CART
  • Partial least squares



LINKS