Jan 10, 2013 Roundup

Here are some things I noticed today that others might benefit from:

Probe to Probe Mapping

Neil Saunders highlighted a problem in software that is supposed to work with different array types, CNAmet:
"the problem of mapping measurements between different array types is not dealt with by CNAmet": or anything else in my experience (link)
There is a software package that does these type of interconversions, Absolute ID Convert, which uses genomic coordinate mapping to interconvert between array IDs. The paper was published in BMC Bioinformatics last year (link) by a PhD student from my group, who has gone on to PostDoc at Harvard.

Sequencing Errors due to Sample Processing

Nick Loman (twitter, blog) has an interesting post highlighting recent developments in errors in Next-Generation Sequencing arising from sample preparation protocols. Casey Bergman is maintaining a collection of papers related to sequencing errors.

Protein Annotation Biases

Iddo Friedberg has a new arXiv preprint examining the effect of biases in the experimental annotations of protein function, and their effect on our understanding of protein function. I haven't read it yet, but from the abstract, it looks like it is definitely something to check out.

Free Statistical Methods Ebook

If you work with any amount of data (likely if you read this blog regularly), then you might be interested in the free ebook of "The Elements of Statistical Learning" (Hastie, Tibshirani, and Friedman), which is a book on a wide variety of machine learning methods, written by experts in the field. I downloaded my copy, you should too.