PLIER - Probe Logaritmic Intensity ERror

[Peter Johansson]

There appear to be two alternative roads to incorporate PLIER.

PLIER is part of APT ​(Affymetrix Power Tools), which is a package of several commandline tools for different kinds of Affy data. As far as I can understand the whole package is licensed under GPL and mostly implemented in C++.

An alternative way appears through BioConductor, where PLIER is downloadable from ​http://www.bioconductor.org/download/oldrelease/bioc1.6/popular/plier.html

Perhaps the latter alternative is preferable as a connection to !BioC is not far away. Yet I present both roads here to let their pros and cons be discussed.

[Peter Johansson]

Using APT (see above) seems to be preferable. Besides PLIER, APT also contain support for RMA, MAS5 detection, MAS5 signal, and DABG (detected above background). The latter ones are perhaps out-dated, but it might be worthwile considering to support RMA through APT.

[Peter Johansson]

Description on PLIER is available here

www.affymetrix.com/support/technical/technotes/plier_technote.pdf

[Peter Johansson]

(In [266]) initial check-in of PLIER refs #45

[Peter Johansson]

(In [271]) Fixing the import into BASE of the results generated by PLIER. Refs #45. I leave this ticket open as documentation still need to be written and the plugin should be tested with a larger number of samples.

[Peter Johansson]

(In [272]) intermediate commit of new installation instructions for affymetrix package refs #45

[Peter Johansson]

(In [273]) some more installation instructions for affymetrix package refs #45

[Peter Johansson]

(In [274]) some more lippstick refs #45

[Peter Johansson]

(In [276]) updated README for affy package refs #45

[Peter Johansson]

(In [277]) some lippstick refs #45

[Peter Johansson]

closed in this release

​http://lev.thep.lu.se/trac/baseplugins/browser/tags/se/lu/thep/affymetrix-0.6

also see

​http://lev.thep.lu.se/trac/baseplugins/wiki/se.lu.thep.affymetrix