269 search results for "PCA"

DESeq vs edgeR Comparison

September 18, 2012
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DESeq vs edgeR Comparison

Update (Dec 18, 2012): Please see this related post I wrote about differential isoform expression analysis with Cuffdiff 2.DESeq and edgeR are two methods and R packages for analyzing quantitative readouts (in the form of counts) from high-throughput e...

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What’s the smallest amount you can’t make with 5 coins ?

September 16, 2012
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What’s the smallest amount you can’t make with 5 coins ?

My amazing, awesome wife often comes up with the little puzzles for our amazing children, and this one seemed destined to be solved in R. So, using up to 5 coins (1p, 2p, 5p, 10p, 20p and 50p) first she asked our kids whether they could make every val...

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Comparing Stan to JAGS for Bayesian Inference (Part 1?)

September 5, 2012
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Comparing Stan to JAGS for Bayesian Inference (Part 1?)

Stan is a new, open source, Bayesian inference tool. Stan is based on the the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo. In order to compare Stan with JAGS, a gibbs sampler approach to Bayesian inference, I used the classic WinBUGS rats example. The rats example uses a hierarchical model to look at...

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Plotting model fits

August 29, 2012
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Plotting model fits

We all know that it is important to plot your data and explore the data visually to make sure you understand it. The same is true for your model fits. First, you want to make sure that the model is fitting...

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Why R for Mass Spectrometrist and Computational Proteomics

August 25, 2012
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Why R for Mass Spectrometrist and Computational Proteomics

Why R:Actually, It is a common practice the integration of the statistical analysis of the resulted data and in silico predictions of the data generated in your manuscript and your daily research. Mass spectrometrist, biologist and bioinformaticians c...

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2014 Winter Olympics: Home Court Advantage – Russia

August 22, 2012
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2014 Winter Olympics: Home Court Advantage – Russia

"Russia is a riddle wrapped in a mystery inside an enigma."  -- Winston Churchill, radio address in 1939 A couple of weeks ago, Graph of the Week published an article describing the significant improvement in medals won by the host...

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ARMA Models for Trading

August 21, 2012
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ARMA Models for Trading

In this tutorial I am going to share my R&D and trading experience using the well-known from statistics Autoregressive Moving Average Model (ARMA). There is a lot written about these models, however, I strongly recommend Introductory Time Series with R, which I find is a perfect combination between light theoretical background and practical implementations in

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read raster data in parallel

August 18, 2012
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read raster data in parallel

Use library(parallel) to read raster data in parallel fashion Use library(parallel) to read raster data in parallel fashion Recently, I have been doing some analysis for a project I am involved in. In particular, I was...

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Adventures at My First JSM (Joint Statistical Meetings) #JSM2012

August 6, 2012
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Adventures at My First JSM (Joint Statistical Meetings) #JSM2012

During the past few decades that I have been in graduate school (no, not literally) I have boycotted JSM on the notion that “I am not a statistician.” Ok, I am a renegade statistician, a statistician by training. JSM 2012 was held in San Diego, CA, one of the best places to spend a week during the summer. This...

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Discriminating Between Iris Species

August 4, 2012
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Discriminating Between Iris Species

The Iris data set is a famous for its use to compare unsupervised classifiers. The goal is to use information about flower characteristics to accurately classify the 3 species of Iris. We can look at scatter plots of the 4 variables in the data set and see that no single variable nor bivariate combination can achieve this. One approach to improve the separation

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