Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Archive for January, 2010

    R script to filter probesets with log-expression values below the lowest spike-in

    27th January 2010

    Sometimes there is a need to remove all the probesets, which have expression values below the minimal spike-in intensity on the Affymetrix microarray. The reasoning behind this procedure is simple: minimal-expression spike-ins represent the bottom margin of microarray sensitivity, and anything below that margin cannot be reliably quantified – which also means that both fold-change and p-value of expression variance will be unreliable for these probesets.

    Here’s a simple R script to do just that. It is abundantly commented, and also contains an optional (commented out) fragment which allows the removal of more low-variance, low-intensity probesets.

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    Posted in Bioinformatics, Programming, Science | No Comments »

    Chandler 1.0.3 package for Debian testing amd64

    25th January 2010

    Recently, I have come across the Chandler project. Chandler is a sophisticated organizer, including tasks, calendar, appointments, invitations, and many more.

    The project does provide a 64-bit package for Ubuntu 8.10 “Intrepid Ibex”, but it has a dependency on python-zope-interface – which in Debian testing is a virtual package, currently provided by python-zope.interface. That single dependency made my aptitude complain all the time, so I edited the .deb-file, renaming depends/python-zope-interface to depends/python-zope.interface (following nice and simple instructions). After that – no more aptitude complaints, and Chandler works fine.

    Download the modified Chandler 1.0.3 Debian testing amd64 package (md5: 239071715977bea2eb75f3bb54491a02).

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    Posted in *nix, Software | 1 Comment »

    Standard deviation and variance in pictures

    24th January 2010

    MathIsFun offers nicely illustrated pages on math, algebra, geometry and maybe more.

    For example, there is a step-by-step instruction on calculating variance and standard deviation for a set of measured dog heights, with a final picture (below) illustrating one-sigma distance from the mean. Unfortunately, concepts of normal distribution and %% of data points within each sigma range are not discussed, but that might as well be too much for a nice explanation. There are also animations, like this mean machine. Overall, MathIsFun is a nice resource for younglings.

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    Posted in Links | No Comments »

    Simple and efficient Drupal upgrades: patch!

    3rd January 2010

    Just a quick note: upgrading Drupal using a patch file is a really efficient and fast method, especially because diff/patch files are available for different Drupal version combinations.

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    Posted in Drupal, Links, Notepad, Web | No Comments »