Articles by R on Guangchuang Yu

[Project Euler] – Problem 57

May 19, 2011 | R on Guangchuang Yu

It is possible to show that the square root of two can be expressed as an infinite continued fraction. √ 2 = 1 + 1/(2 + 1/(2 + 1/(2 + … ))) = 1.414213… By expanding this for the first four iterations, we get: Read More: 547 Words Totally [Read more...]

clusterProfiler in Bioconductor 2.8

March 26, 2011 | R on Guangchuang Yu

In recently years, high-throughput experimental techniques such as microarray and mass spectrometry can identify many lists of genes and gene products. The most widely used strategy for high-throughput data analysis is to identify different gene clusters based on their expression profiles. Another commonly used approach is to annotate these genes ... [Read more...]

Machine Learning Ex2 – Linear Regression

March 22, 2011 | R on Guangchuang Yu

Thanks to this post, I found OpenClassroom. In addition, thanks to Andrew Ng and his lectures, I took my first course in machine learning. These videos are quite easy to follow. Exercise 2 requires implementing gradient descent algorithm to model data with linear regression. Read More: 243 Words Totally [Read more...]

Estimate Probability and Quantile

January 25, 2011 | R on Guangchuang Yu

Simple root finding and one dimensional integrals algorithms were implemented in previous posts. These algorithms can be used to estimate the cumulative probabilities and quantiles. Here, take normal distribution as an example. Read More: 281 Words Totally [Read more...]

Single variable optimization

January 1, 2011 | R on Guangchuang Yu

Optimization means to seek minima or maxima of a funtion within a given defined domain. If a function reach its maxima or minima, the derivative at that point is approaching to 0. If we apply Newton-Raphson method for root finding to f’, we can get the optimizing f. Read More: 223 Words ... [Read more...]

one-dimensional integrals

December 25, 2010 | R on Guangchuang Yu

The foundamental idea of numerical integration is to estimate the area of the region in the xy-plane bounded by the graph of function f(x). The integral was esimated by divide x to small intervals, then add all the small approximations to give a total approximation. Read More: 468 Words Totally [Read more...]

Project Euler — Problem 187

December 23, 2010 | R on Guangchuang Yu A composite is a number containing at least two prime factors. For example, 15 = 3 × 5; 9 = 3 × 3; 12 = 2 × 2 × 3. There are ten composites below thirty containing precisely two, not necessarily distinct, prime factors: 4, 6, 9, 10, 14, 15, 21, 22, 25, 26. Read More: 671 Words Totally [Read more...]

Root finding

December 4, 2010 | R on Guangchuang Yu

Numerical root finding methods use iteration, producing a sequence of numbers that hopefully converge towards a limits which is a root. In this post, only focus four basic algorithm on root finding, and covers bisection method, fixed point method, Newton-Raphson method, and secant method. Read More: 1896 Words Totally [Read more...]

The avalanche of publications mentioning GO

November 30, 2010 | R on Guangchuang Yu

Gene Ontology is the de facto standard for annotation of gene products. It has been widely used in biological data mining, and I believe it will play more central role in the future. Publications mentioning GO was collected and deposited in GO ftp, and can be accessed (ftp://ftp.geneontology.... [Read more...]

The S3 OOP system

October 15, 2010 | R on Guangchuang Yu

R currently supports two internal OOP systems (S3 and S4), and several others as add-on packages, such as R.oo, and OOP. S3 is easy to use but not reliable enough for large software projects. The emphasis of the S3 system was on generic functions and polymorphism. It’s a ... [Read more...]
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