133 search results for "heatmap"

Another look at over-representation analysis interpretation

May 21, 2012
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Another look at over-representation analysis interpretation

Interpreting a list of differentially regulated genes can take many forms. One of the most widely used method is looking for enrichment of functional group of genes compared to a random sampling of gene from the same universe, namely an over-representation analysis (ORA).The point I want to explore today is what is the best way to interpret the results...

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More Bixi Data Visualization

May 17, 2012
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More Bixi Data Visualization

I mentioned in a previous post that our team at the recent Hack/Reduce hackathon had some fun with a data set which consisted of Bixi station states at minute level temporal resolution. In addition to pulling out and plotting the flux at each station on an hourly basis, we also plotted the system state (number

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Clustering analysis and its implementation in R

April 29, 2012
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Earlier I posted a blog for "k-means + heatmap" used for clustering analysis. Recently to prepare for the "Bioinformatics Tools" meeting, I made a slide with more details on "clustering analysis". Here it is:https://docs.google.com/presentation/d/1vMS3...

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Heat map visualization of sick day trends in Finland with R, ggplot2 and Google Correlate

April 24, 2012
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Heat map visualization of sick day trends in Finland with R, ggplot2 and Google Correlate

Inspired by Margintale’s post “ggplot2 Time Series Heatmaps” and Google Flu Trends I decided to use a heat map to visualize sick days logged by HeiaHeia.com Finnish users. I got the data from our database, filtering results by country (Finnish users only) in a tab separated form with the first line as the header. Three columns

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118 years of US State Weather Data

April 22, 2012
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118 years of US State Weather Data

A recent post on the Junkcharts blog looked at US weather dataand the importance of explaining scales (which in this case went up to 118). Ultimately, it turns out that 118 is the rank of the data compared to the previous 117 years of data (in ascending order, so that 118 is the highest). At … Continue reading...

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Simulated Annealing in Julia

April 4, 2012
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Simulated Annealing in Julia

Building Optimization Functions for Julia In hopes of adding enough statistical functionality to Julia to make it usable for my day-to-day modeling projects, I’ve written a very basic implementation of the simulated annealing (SA) algorithm, which I’ve placed in the same JuliaVsR GitHub repository that I used for the code for my previous post about

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R 2.15.0 is released

March 30, 2012
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R 2.15.0 is released

Bellow is the announcement made by Peter Dalgaard: The build system rolled up R-2.15.0.tar.gz (codename “Easter Beagle”) at 9:00 this morning. This is the first release of the 2.15 series and contains several new features and changes; see the list below for details. You can get the source code from http://cran.r-project.org/src/base/R-2/R-2.15.0.tar.gz or wait for it to be mirrored at...

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Functional regression, INLA, and how to build the World’s Slowest Fourier Transform

March 29, 2012
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Functional regression, INLA, and how to build the World’s Slowest Fourier Transform

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Visualising Twitter User Timeline Activity in R

February 17, 2012
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Visualising Twitter User Timeline Activity in R

I’ve largely avoided “time” in R to date, but following a chat with @mhawksey at #dev8d yesterday, I went down a rathole last night exploring a few ways of visualising a Twitter user timeline and as a result also had a quick initial play with some time handling features of R, such as timeseries objects,

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Revisiting homicide rates

February 10, 2012
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Revisiting homicide rates

A pint of R plotted an interesting dataset: intentional homicides in South America. I thought the graphs were pretty but I was unhappy about the way information was conveyed in the plots; relative risk should be very important but number … Continue reading →

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