Opened 17 years ago
Closed 16 years ago
#45 closed task (fixed)
PLIER - Probe Logaritmic Intensity ERror
Reported by: | Peter Johansson | Owned by: | Peter Johansson |
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Priority: | major | Milestone: | |
Component: | se.lu.thep.affymetrix | Keywords: | |
Cc: |
Description (last modified by )
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 17 years ago by
Description: | modified (diff) |
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comment:2 Changed 17 years ago by
Owner: | changed from Jari Häkkinen to Peter Johansson |
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Status: | new → assigned |
comment:3 Changed 17 years ago by
Description on PLIER is available here
www.affymetrix.com/support/technical/technotes/plier_technote.pdf
comment:5 Changed 16 years ago by
comment:6 Changed 16 years ago by
comment:7 Changed 16 years ago by
comment:11 Changed 16 years ago by
comment:12 Changed 16 years ago by
Resolution: | → fixed |
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Status: | assigned → closed |
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.