Opened 15 years ago

Closed 14 years ago

#45 closed task (fixed)

PLIER - Probe Logaritmic Intensity ERror

Reported by: Peter Johansson Owned by: Peter Johansson
Priority: major Milestone:
Component: se.lu.thep.affymetrix Keywords:
Cc:

Description (last modified by 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.

Change History (12)

comment:1 Changed 15 years ago by Peter Johansson

Description: modified (diff)

comment:2 Changed 15 years ago by Peter Johansson

Owner: changed from Jari Häkkinen to Peter Johansson
Status: newassigned

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.

comment:3 Changed 15 years ago by Peter Johansson

Description on PLIER is available here

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

comment:4 Changed 14 years ago by Peter Johansson

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

comment:5 Changed 14 years ago by 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.

comment:6 Changed 14 years ago by Peter Johansson

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

comment:7 Changed 14 years ago by Peter Johansson

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

comment:8 Changed 14 years ago by Peter Johansson

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

comment:9 Changed 14 years ago by Peter Johansson

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

comment:10 Changed 14 years ago by Peter Johansson

(In [277]) some lippstick refs #45

comment:12 Changed 14 years ago by Peter Johansson

Resolution: fixed
Status: assignedclosed
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