GeneTitan artifacts II

Friday, January 28th, 2011 by hinrich


I have previously discussed that the new Affymetrix GeneTitan system for generating whole genome transcriptional profiles in a 96-well plate likely has different artifacts than the regular cartridge arrays.

We have made a first version of a R library called TitanQC available via R-Forge. The package contains various functions to look into potential spatial effects on the 96-well plate. Graphics visualizing the individual intensity distributions per sample, median raw probe intensities, but also an overall image of individual affyPLM images ordered according to their respective position within the plate are included.

Please beware that the package is not yet finished. We still need to work on the documentation. You can find the home page of the project on R-Forge here.

Posted in Molecular Profiling

4th La Calestienne

Thursday, January 20th, 2011 by hinrich

4th La Calestienne

Drug discovery is a pre-clinical activity that takes approximately five years until a new medical entity (NME) is developed. Several aspects of this process need to be optimized. We have identified the following problems that we would like to address with a new research & development project:

• the time gap between the selection of a lead compound and the detection of side effects
• missed opportunities of deselecting compounds that might initially have a poorer target-related activity but a preferable side activity profile
• the lack of cellular activity assays during the early stages of drug discovery

The new project has been proposed to the Flamish IWT. If accepted, we will aim to make the first steps towards addressing these problems by linking whole genome expression profiling with chemical properties. The two year project will focus on the analysis of a few chemotypes (chemical core structures) to assess whether compound-induced changes in transcriptional activity could aid in the optimization of chemical structures.

For this we will meet at La Calestienne in February to brainstorm our initial experimental approaches and discuss possible statistical and data analytical approaches.

Posted in Science

LyX for Kids

Wednesday, January 19th, 2011 by hinrich


My oldest son has to write a first small working paper. He is eight years old. Of course, his school is using Microsoft Word.

This made me wonder: The purpose of a computer is to make your life easier and take over work from you whenever possible. Why do we still teach kids the old way of writing documents? Maybe because there is no alternative?

There is LyX. However, it is unusual to work with, but - thanks to the magic of LaTeX - actually does a better job in helping you structure your work, focus on writing and still get a professionally looking result.

Therefore I suggest to develop a new simple front end to get kids (grown ups are already too much biased to the MS Word way) started onto this better way of writing documents.

Posted in Society