resources
presentations
Let me tell you about something.
lunch break
Distractions and amusements, with a sandwich and coffee.
Alex — Internet's Most Popular Rat
Poster Rat for Rat Genome Sequencing
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The rat genome sequencing project at the Baylor College of Medicine Human Genome Sequencing Centre is complete. The genome has been analyzed and published. I'd like to introduce you one of the faces of the project: Alex, the genomics rat idol. Arguably, Alex is the most popular rat on the internet. For the justification of this strong statement, read on. 
▲ Alex, the rat. Rattus norvegicus on an ABI 3700 genome sequencer.
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▲ Alex, the rat. Rattus norvegicus on an ABI 3700 genome sequencer.
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Alex's BiographyAlex was born in May 2000. It's well known that a rat's cuteness reaches maximum at about 3-4 weeks. After this critical time, a pet store rat is less likely to be purchased and may be asked to act as snake food. In Alex's case, she was perilously close to her deadline. Luckily for her, we paid a ransom of $6.99 to the Noah's Ark pet shop in Vancouver. She was on her last cute leg. 
▲ Portrait of Alex, the genome rat (Rattus norvegicus). Here, she is seen in a forced portrait position
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From May 2000 Alex spent most of her time hoarding food pellets and riding on shoulders. 
▲ Portrait of Alex, the genome rat (Rattus norvegicus). Riding on shoulder.
Alex liked to bite. And rats only bite hard — they don't nibble. Her contention for this unattractive behaviour was the uncanny similarity between a finger and a pellet of food. Other than unpredictable bouts of biting (by far the most exciting aspect of her personality), Alex lacked other distinguishing characteristics. Alex died of a seizure in late 2002. She was buried outside of the Museum of Anthropology. A ratty pair of underwear served as a burial shroud. And I hope you got that last pun. |
DOWNLOAD ALL PHOTOS.
Photos are for public use. Use, modification and distribution of these photos is unrestricted. Alex's PopularityDespite my best efforts at meaningful work, this web page continues to be the most popular of all my online offerings, making for a somewhat embarrassing achievement. Alex's images consistently show up first in Google's web search for 'rat', 'rat image' and image search for 'rat'. 
▲ Alex image is the first for Google's 'rat' search query (retrieved 16 Mar 2013).
(rat Google search)
▲ Alex image is the first for Google's 'rat image' search query (retrieved 16 Mar 2013).
(rat Google search)
Finally, Alex appears as the first entry in Google images for 'rat'. 
▲ Alex image is the first for Google's 'rat image' search query (retrieved 16 Mar 2013).
(rat Google search)
Alex's Public AppearancesAlex is neither without modesty nor public fame. Her first cover-ratgirl appearance was on the April 2004 issue of Genome Research. 
▲ Alex the rat appeared on the cover of Genome Research (April 2004).
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More recently, she's appeared on the cover of Ethnologie Francaise (Jan-Mar 2009 issue). 
▲ Alex the rat appeared on the cover of Ethnologie Francaise (1/2009).
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The topic of the issue was the relationship between animals and humans. It is fitting therefore to recount here the relationship I shared with Alex during her sojourn with us. |
news + thoughts
Mind your p's and q's
In the April Points of Significance Nature Methods column, we continue our and consider what happens when we run a large number of tests.
Observing statistically rare test outcomes is expected if we run enough tests. These are statistically, not biologically, significant. For example, if we run N tests, the smallest P value that we have a 50% chance of observing is 1–exp(–ln2/N). For N = 10k this P value is Pk=10–kln2 (e.g. for 104=10,000 tests, P4=6.9×10–5).
We discuss common correction schemes such as Bonferroni, Holm, Benjamini & Hochberg and Storey's q and show how they impact the false positive rate (FPR), false discovery rate (FDR) and power of a batch of tests.
Krzywinski, M. & Altman, N. (2014) Points of Significance: Comparing Samples — Part II — Multiple Testing Nature Methods 11:215-216. Krzywinski, M. & Altman, N. (2014) Points of Significance: Comparing Samples — Part I — t-tests Nature Methods 11:215-216. Krzywinski, M. & Altman, N. (2013) Points of Significance: Significance, P values and t-tests Nature Methods 10:1041-1042.
Happy Pi Day— go to planet π
Celebrate Pi Day (March 14th) with the art of folding numbers. This year I take the number up to the Feynman Point and apply a protein folding algorithm to render it as a path.
For those of you who liked the minimalist and colorful digit grid, I've expanded on the concept to show stacked ring plots of frequency distributions.
And if spirals are your thing...
Have data, will compare
In the March Points of Significance Nature Methods column, we continue our discussion of t-tests from November (Significance, P values and t-tests).
We look at what happens how uncertainty of two variables combines and how this impacts the increased uncertainty when two samples are compared and highlight the differences between the two-sample and paired t-tests.
When performing any statistical test, it's important to understand and satisfy its requirements. The t-test is very robust with respect to some of its assumptions, but not others. We explore which.
Krzywinski, M. & Altman, N. (2014) Points of Significance: Comparing Samples — Part I Nature Methods 11:215-216.
Krzywinski, M. & Altman, N. (2013) Points of Significance: Significance, P values and t-tests Nature Methods 10:1041-1042.