Blog Archives

A minor update to my “apply functions” post

February 27, 2014
By
A minor update to my “apply functions” post

One of my more popular posts is A brief introduction to “apply” in R. Come August, it will be four years old. Technology moves on, old blog posts do not. So: thanks to BioStar user zx8754 for pointing me to this Stack Overflow post, in which someone complains that the code in the post does

Read more »

Box plots. Like box plots, only…box plots.

February 2, 2014
By
Box plots. Like box plots, only…box plots.

On a rare, brief holiday (here and here, if you’re interested; both highly-recommended), I make the mistake of checking my Twitter feed: paging @neilfws . . . RT @psudmant: Ground breaking new methods from @naturemethods – boxplots – no rly nature.com/nmeth/journal/…— Chris Miller (@chrisamiller) January 30, 2014 This points me to BoxPlotR. It draws box

Read more »

BLATting the internet: the most frequent gene?

January 23, 2014
By
BLATting the internet: the most frequent gene?

I enjoyed this story from the OpenHelix blog today, describing a Microsoft Research project to mine DNA sequences from web pages and map them to UCSC genome builds. Laura DeMare asks: what was the most-hit gene? Most hit gene? APOE? MT @GenomeBrowser We BLATed the Internet! DNA sequences from 40 billion webpages mapped to hg19

Read more »

Quilt plots. Like heat maps, only…heat maps

January 15, 2014
By
Quilt plots. Like heat maps, only…heat maps

Stephen tweets: Quilt Plots: A Simple Tool for the #Visualisation of Large Epidemiological Data buff.ly/1doSx4X— Stephen Rudd (@SAGRudd) January 15, 2014 Quilt plots. Sounds interesting. The link points to a short article in PLoS ONE, containing a table and a figure. Here is Figure 1. If you looked at that and thought “Hey, that’s a

Read more »

R: how not to use savehistory() and source()

December 2, 2013
By
R: how not to use savehistory() and source()

Admitting to stupidity is part of the learning process. So in the interests of public education, here’s something stupid that I did today. You’re working in the R console. Happy with your exploratory code, you decide to save it to a file. Then, you type something else, for example: And then, decide that you should

Read more »

Bacteria and Alzheimer’s disease: I just need to know if ten patients are enough

October 29, 2013
By
Bacteria and Alzheimer’s disease: I just need to know if ten patients are enough

You can guarantee that when scientists publish a study titled: Determining the Presence of Periodontopathic Virulence Factors in Short-Term Postmortem Alzheimer’s Disease Brain Tissue a newspaper will publish a story titled: Poor dental health and gum disease may cause Alzheimer’s Without access to the paper, it’s difficult to assess the evidence. I suggest you read

Read more »

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

August 21, 2013
By
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

Read more »

Interestingly: the sentence adverbs of PubMed Central

July 15, 2013
By
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,

Read more »

-omics in 2013

June 24, 2013
By
-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

Read more »

Using the Ensembl Variant Effect Predictor with your 23andme data

June 3, 2013
By
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

Read more »