leaf area measuring — R package “EBImage”

July 9, 2012 | Tony

Besides microscopic images in our routine, common photos are frequently taken to measure quantitative plant features, such as leaf area, root length, branch numbers, etc. Scientific software is available for manual processing. For example, to measure the root length, one need to use the … Continue reading → [Read more...]

automated cell phenotyping — R package “EBImage”

July 5, 2012 | Tony

Counting cells under microscope is always laborious and null. Those in the art would be relieved with assistance of a powerful image processing package, EBImage. Images are treated as “Image” objects, essentially multi-dimensional arrays. The class “Image” contains spatial information, pixel … Continue reading → [Read more...]

GEO database: curation lagging behind submission?

August 30, 2010 | nsaunders

I was reading an old post that describes GEOmetadb, a downloadable database containing metadata from the GEO database. We had a brief discussion in the comments about the growth in GSE records (user-submitted) versus GDS records (curated datasets) over time. Below, some quick and dirty R code to examine the ... [Read more...]

biomaRt and GenomeGraphs: a worked example

June 6, 2010 | nsaunders

As promised a few posts ago, another demonstration of the excellent biomaRt package, this time in conjunction with GenomeGraphs. Here’s what we’re going to do: Grab some public microarray data Normalise and get a list of the most differentially-expressed probesets Use biomaRt to fetch the genes associated with ... [Read more...]

Beware of rogue header files (Bioconductor installation)

May 11, 2010 | nsaunders

Just a short note concerning a “gotcha”. As I have many times before, I opened an R console on my newly-upgraded (to lucid 10.04) Ubuntu machine, typed source(“”) and began a Bioconductor install with biocLite(). Only this time, I saw this: Error in dyn.load(file, ... [Read more...]

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