Blog Archives

Microarrays, scan dates and Bioconductor: it shouldn’t be this difficult

August 21, 2013
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Microarrays, scan dates and Bioconductor: it shouldn’t be this difficult

When dealing with data from high-throughput experimental platforms such as microarrays, it’s important to account for potential batch effects. A simple example: if you process all your normal tissue samples this week and your cancerous tissue samples next week, you’re in big trouble. Differences between cancer and normal are now confounded with processing time and

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Interestingly: the sentence adverbs of PubMed Central

July 15, 2013
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Interestingly: the sentence adverbs of PubMed Central

Scientific writing – by which I mean journal articles – is a strange business, full of arcane rules and conventions with origins that no-one remembers but to which everyone adheres. I’ve always been amused by one particular convention: the sentence adverb. Used with a comma to make a point at the start of a sentence,

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-omics in 2013

June 24, 2013
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-omics in 2013

Just how many (bad) -omics are there anyway? Let’s find out. 1. Get the raw data It would be nice if we could search PubMed for titles containing all -omics: However, we cannot since leading wildcards don’t work in PubMed search. So let’s just grab all articles from 2013: and save them in a format

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Using the Ensembl Variant Effect Predictor with your 23andme data

June 3, 2013
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Using the Ensembl Variant Effect Predictor with your 23andme data

I subscribe to the Ensembl blog and found, in my feed reader this morning, a post which linked to the Variant Effect Predictor (VEP). The original blog post, strangely, has disappeared. Not to worry: so, the VEP takes genotyping data in one of several formats, compares it with the Ensembl variation + core databases and

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A brief note: R 3.0.0 and bioinformatics

April 3, 2013
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A brief note: R 3.0.0 and bioinformatics

Today marks the release of R 3.0.0. There will be plenty of commentary and useful information at sites such as R-bloggers (for example, Tal’s post). Version 3.0.0 is great news for bioinformaticians, due to the introduction of long vectors. What does that mean? Well, several months ago, I was using the simpleaffy package from Bioconductor

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R/ggplot2 tip: aes_string

February 25, 2013
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R/ggplot2 tip: aes_string

I’m a big fan of ggplot2. Recently, I ran into a situation which called for a useful feature that I had not used previously: aes_string. Imagine that you have data consisting of observations for several variables – let’s say A, B, C – where each observation is from one of two groups – call them

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Basic R: rows that contain the maximum value of a variable

February 12, 2013
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Basic R: rows that contain the maximum value of a variable

File under “I keep forgetting how to do this basic, frequently-required task, so I’m writing it down here.” Let’s create a data frame which contains five variables, vars, named A – E, each of which appears twice, along with some measurements: Now, let’s say we want only the rows that contain the maximum values of

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Addendum to yesterday’s post on custom CSS and R Markdown

August 27, 2012
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Addendum to yesterday’s post on custom CSS and R Markdown

Updates from RStudio support: (1) “Thanks for reporting and I was able to reproduce this as well. I’ve filed a bug and we’ll take a look.” (2) Taking a further look, this is actually a bug in the Markdown package and we’ve asked the maintainer (Jeffrey Horner) to look into it. As juejung points out

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Custom CSS for HTML generated using RStudio

August 26, 2012
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Custom CSS for HTML generated using RStudio

People have been telling me for a while that the latest version of RStudio, the IDE for R, is a great way to generate reports. I finally got around to trying it out and for once, the hype is justified. Start with this excellent tutorial from Jeremy Anglim. Briefly: the process is not so different

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Twitter coverage of the ISMB 2012 meeting: some statistics

August 15, 2012
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Twitter coverage of the ISMB 2012 meeting: some statistics

OK, let’s do this: some statistics and visualization of the tweets for ISMB 2012. First, thanks to Stephen Turner who got things started in this post at his excellent blog, Getting Genetics Done. Subscribe to his feed if you don’t already do so. I’ve created a Github repository for this project (and future Twitter-related work).

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