Math 283 - Spring 2012 - Statistical Methods in Bioinformatics

Statistics

Rice Virtual Lab in Statistics. Includes an online statistics book, HyperStat Online, and demos of statistical concepts, such as the Normal Approximation to the Binomial Distribution.
Birthday problem at Mathworld and at the Mathematical Association of America.
Web-based calculators for different statistical functions at UCLA and an index of similar sites.
Football games that predict presidential elections, and other bizarre correlations: article 1, article 2 (these are news/opinion articles, not academic/scientific sites).
How the Gallup poll works (includes examples of sampling issues and margin of error): follow the links for "How does Gallup Polling work?" or other questions on the Gallup Poll website's FAQ.

Short readable summary of controversial statistical issues in Mendel's work, by Madan Bhattacharyya, Iowa State University.
A list of papers about both sides of the controversy.
English translation of Mendel's second paper.
Transcription of Fisher's paper that analyzed Mendel's data in the above paper.

Entrez-Genome at NCBI. Includes the DNA sequences of many organisms, tools for viewing them, and analysis. Sample genomes include SARS and E. Coli.
Mouse Genome Informatics.

National Human Genome Research Institute (NIH/NHGRI): Approved Sequencing Targets.
List of genome sequencing projects funded by NIH.
Genome 10K Project: Sequencing species lists
Vertebrate sequencing projects planned by different organizations.
Broad Institute: 29 Mammals Project
Beijing Genomics Institute (BGI)

Pictures of Microarrays: Affymetrix Image Library and Terry Speed's Lab have pictures of microarrays.
The Stanford MicroArray Database has microarray pictures and data. For the Perou et al. experiment, pick experimenter PEROU and hit Display Data. For the Nielsen et al. paper, pick experimenter MRIJN.
Articles (you may need to use a UCSD network proxy or VPN to access these from home):
- Hedenfelk, et al. article on breast cancer.
- Armstrong, et al. article on Leukemia
- Perou, et al. article on breast tumors. Also see the Stanford Microarray database (above) for the microarray data and here for pictures of the tissue samples.
- Storey, et al. paper on statistical issues.

Nielsen, et al. paper using SVD in a microarray experiment. Also see the Stanford Microarray database (above) for data, and here for supplementary information.
More SVD and GSVD microarray papers are here.
Orly Alter's website with many papers describing SVD for microarrays.
Yeung and Ruzzo Bioinformatics paper describing PCA for microarrays as problematic.
Todd Will's tutorial on SVD, including interactive Java applet demonstrations.
Example of PCA with Matlab code.

Commercial product. Discounted student version sold at UCSD bookstore.
Installed in ACMS computer labs in AP&M B349 (Windows), B432 (Windows), B325 (dual boot Windows/Linux).
General Matlab documentation
Statistics toolbox
Matlab/R tutorial
The GUI version of Matlab has help available through a menu.
At the command line, help is available via
help sum
(where sum is replaced by the exact command name or topic).

R Project homepage and free download site (Windows, Mac, Linux).
Official documentation is included in the downloadable R package. The R Project homepage includes several types of documentation. See the FAQs and manuals, particularly the introduction and the R language manuals.
Unofficial documentation:
Reference card
Short list of R commands
Tutorial
Quick-R
Array of multiple figures in a single window
Multiple Plots in a Figure
Matlab/R tutorial
The GUI version of R has help available through a menu.
At the command line, help is available via these four forms:
help(sum) help("sum") ?sum ?"sum"
(where sum is replaced by the command you want).
Use the quoted forms if you get syntax errors, e.g., for reserved words and symbols: ?+ and ?if fail but ?"+" and ?"if" work.
It gives an error if you don't know the exact name of the function:
?negative gives an error
help.search("negative") suggests topics related to "negative"