Cohen Lab In The Department of Pediatrics

Software Tools

Code History

A glitch in the release of version 1.3 was corrected on 7/22. This fixes the warning about unequal length in the Chi-Squared test.

Version 1.3 released 7/20/05 with several changes to make it easier to handle data from different chips or fractions.

I. Simultaneous Spectrum Analysis

Source code, binaries, and example data for "Improving feature detection and analysis in SELDI-TOF mass spectra."

Instructions for download and use

R-language source code:

R source (Version 1.3, as of 7/20/05)
R example (Version 1.3, as of 7/20/05)

C DLL binaries:

Binary for R, (version 1.2.1 as of 6/16/05) compiled in Visual C++ 6.0 on Windows XP Professional SP2 (Microsoft Corp)

Example data - Spectra from the paper, 3rd fraction CM10:

Example data - A set of 22 spectra used in the paper, from the 4th fraction on IMAC30 chips, of which one failed spectrum is bad. This demonstrates the use of the chi-squared test to identify bad spectra.

C source code:

C source for the R DLL (version 1.2.1 as of 6/15/05)
C header for the R DLL
.DEF file for the R DLL (version 1.2.1 as of 6/15/05)

II. Clustering

Source code and examples for "Using Clustering to Unravel Correlations in Proteomic Data."

R-language source code:

R source
R example

Example data

KD.txt (text file)
KD.RData
(RData file)

III. Supervised Learning Techniques

Source code for some basic statistical functions, and example data and code for an analysis using several classification techniques.

R-language code:

Example:

analysisCode.R
data_training.txt
data_testing.txt

Please send suggestions, bug reports, or questions regarding sections I and II to Scott Carlson (smcarlson "at" gmail "dot" com) and regarding section III to Ryan Tibshirani (ryantibs "at" stanford "dot" edu).

Copyright Notice: All source code, compiled libraries, and webpage contents are copyright the Harvey Cohen, Department of Pediatrics at Stanford University. All copyright material is free for non-commercial use with correct citation, commercial use is allowed only with the express permission of Dr. Harvey Cohen.

Last updated 12:53 pm June 27th, 2006.

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