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Bioconductor Changlog.
Sat, 01 Mar 2008
affycomp
Fixed usage of se.exprs in ExpressionSet class.
Biostrings
[comments for previous commit + this commit]
- Added the trim() function for trimming the "out of limits" views of a
BStringViews object.
- Now the BStringSet() constructor (and family):
(1) fully supports BStringViews input,
(2) has a 'use.names' argument.
- Support the 'use.names' argument in the "unlist" method for ViewsIndex
objects.
Ringo
fixed bug in function posToProbeAnno
added arguments for users to handle uniqueness of probe matches
affxparser
Version: 1.11.5 [2008-02-29]
o Updated cdfMergeStrands() to merge any even number of groups,
not only units with two or four group pairs.
o BUG FIX: The code in findFiles() for testing if R.utils is loaded
or not in v1.11.4 was not correct making it fail to detect R.utils.
Version: 1.11.4 [2008-02-20]
o Now findFiles() and hence findCdf() is only utilizing the R.utils
package if it is already loaded. It will no longer try to load R.utils.
o Added argument 'allFiles=TRUE' to findFiles().
o Updated readCcg() according to the newer file format specifications.
Now it is possible to do low-level reading of copy-number CNCHP
files generated by the Affymetrix Genotype Console v2.
ABarray
Removed reference to se.exprs since it is no longer relevant.
pathRender
news file -- compliant?
suport for plotExG
various elements added to support plotExGraph
graph
minor problem in pancrCaIni.Rd
MAPKsig graph data is misleading; pancrCaIni pathway graph example to supersede