Learning to use biomaRt

In the past I've been manually downloading tables of data annoation and parsing them with Perl. I guess it's time to do things more elegantly. Below is code taken from the biomaRt vignette: Note If you are using Ubuntu and getting a "Cannot find xml2-config" problem while installing XML, a prequisite to biomaRt, try installing...

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Making a barplot in R

Just a short post on making a barplot in R after reading in data via the read.table() function. I created a file with two rows, the first row containing the header and the second row containing the data values. a b c d e 10 20 30 20 10 Horizontal barplot sorted by values

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Comparing different distributions

I recently learned of the Kolmogorov-Smirnov Test and how one can use it to test whether two datasets are likely to be different, i.e. comparing different distributions. Strictly speaking, the p-value gives us a probability of whether or not we can reject the null hypothesis, which is that two datasets have the same distribution. Using...

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I've joined Twitter

Today while reading a paper, I found some interesting one-liner facts. They are way too short to create a post on but I would like to make a repository of them. What better place to store these facts than Twitter! You can follow me on Twitter for a list of facts on molecular biology and...

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Variance in RNA-Seq data

Updated 2014 April 18th For this post I will use data from this study, that has been nicely summarised already to examine the variance in RNA-Seq data. Briefly, the study used LNCaP cells, which are androgen-sensitive human prostate adenocarcinoma cells, and treated the cells with DHT and with a mock treatment as the control. The...

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Creating a matrix of scatter plots in R

Scatter plots are 2 dimensional plots that show the relationship between two variables. Here I demonstrate how we can create a matrix of scatter plots in R for datasets that have more than two variables. This is particularly useful when we want to visually inspect whether there are associations between variables. #store random set of...

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