Posts Tagged ‘ computing ’

Statistical Analysis StackExchange site now available

July 26, 2010
By
Statistical Analysis StackExchange site now available

The Q&A site for statistical analysis, data mining, data visualization, and everything else to do with data analysis has finally been launched. Please head over to stats.StackExchange.com and start asking and answering questions. Also, spread the word to everyone else who may be interested — work colleagues, students, etc. The more people who use the

Read more »

More StackExchange sites

July 16, 2010
By
More StackExchange sites

The StackExchange site on Statistical Analysis is about to go into private beta testing. This is your last chance to commit if you want to be part of the private beta testing. Don’t worry if you miss out — it will only be a week before it is then open to the public. There is

Read more »

Stack exchange for statistical analysis needs you!

June 17, 2010
By
Stack exchange for statistical analysis needs you!

The proposal to create a StackExchange site for statistical analysis is steadily moving forward. We have now completed the scoping stage which involved finding enough people willing to express an interest in the idea, and voting on some example questions to define what is allowed and what is not allowed on the site. The on-topic

Read more »

Beware of rogue header files (Bioconductor installation)

May 11, 2010
By
Beware of rogue header files (Bioconductor installation)

Just a short note concerning a “gotcha”. As I have many times before, I opened an R console on my newly-upgraded (to lucid 10.04) Ubuntu machine, typed source(“http://bioconductor.org/biocLite.R”) and began a Bioconductor install with biocLite(). Only this time, I saw this: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio/libs/affyio.so':

Read more »

Stata Fail

March 10, 2010
By
Stata Fail

From a recent mailing from Stata (highlighting by me): Funnily enough, there is a Daniel Rubin, a bio-informatics person here at Stanford.

Read more »

principal components and image reconstruction

March 9, 2010
By
principal components and image reconstruction

Jeff Lewis at UCLA told me he teaches principal components with an image reconstruction example. This got me inspired to try it myself. A snapshot appears below, showing how the image quality improves quickly with a relatively small number of principal components. A full, Sweaved write up is here, making use of the biOps package

Read more »

sequential ideal point estimates

January 9, 2010
By
sequential ideal point estimates

Out of curiosity, I produced a “sequential” set of ideal point estimate for the (current) 111th U.S. Senate, plotting the results in the graph attached below (click on the thumbnail); as is conventional, red is Republican and blue is Democratic. The analysis uses all 373 non-unanimous roll calls in the 111th Senate thus far. Each

Read more »

Samples per series/dataset in the NCBI GEO database

January 7, 2010
By
Samples per series/dataset in the NCBI GEO database

Andrew asks: I want to get an NCBI GEO report showing the number of samples per series or data set. Short of downloading all of GEO, anyone know how to do this? Is there a table of just metadata hidden somewhere? At work, we joke that GEO is the only database where data goes in,

Read more »

APIs: I wish the life sciences would learn from social networks

December 10, 2009
By
APIs: I wish the life sciences would learn from social networks

I was prompted by a thread on the apparent decline of FriendFeed to look for evidence of declining participation in my networks. First, a quick and dirty Ruby script, tls.rb to grab the Life Scientists feed and count the likes and comments: #!/usr/bin/ruby require 'rubygems' require 'json/pure' require 'net/http' require 'open-uri' def format_date(d) if d

Read more »

A brief survey of R web interfaces

November 29, 2009
By
A brief survey of R web interfaces

I’m looking at ways to provide access to R via a web application. First rule: see what’s available first, before you reinvent the wheel. It’s not pretty. From the R Web Interfaces FAQ: Software Brief notes Rweb Page last updated 1999. Of the 3 example links on the page one ran very slowly, the second not at

Read more »