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Bioconductor Changlog.
Thu, 05 Jun 2008
flowViz
making sure we get a reasonable variance estimate in the timeLinePlots
fixed bug in desnityplot
limma
4 June 2008: limma 2.15.7
- new S3 generic function avereps() for averaging over irregularly
spaced replicate spots. A method is defined for MAList objects
and a default method intended for matrices.
Minor cleaning: tabs instead of spaces for indentation in two places
flowCore
fixed bug in splitting of flowSets by factors
ShortRead
sync configure with configure.ac
Use configure to add -lz to package library path
BCRANK
penalties P1 and P2 are now optional
Biostrings
Add vcountPattern, to count occurrend of pattern in XStringSet-derived
objects
Pushed PairwiseAlignment S4 object creation to C level in preparation for a time when the output is vectorized to a greater extent.
Fixed a bug when aligning an empty string.
ArrayExpress
Remove the ArrayExpress2 function which becomes useless
Extend ArrayExpress function to other data types than affy. Functions based on the QT and the scanner name.
[/ArrayExpress] permanent link
flowUtils
Removing empty files.
vsn
addVigs2WinMenu.
I fixed the Makefile in inst/doc so that Rplots.pdf is now also deleted.
I changed the vignette such that the scatterplots with many dots are now
written as PNG rather than PDFs.
==> The built package of this version of vsn has now a size of 1.2MB
instead of 5.5MB.
dualKS
This adds dualKS to the package repository.
flowDB
Correcting the name of the package in the DESCRIPTION file.
SNPchip
fix bug in .plot when genotype calls are not available
xcms
Fix includeMSn handling in xcmsSet + Graphviz fix + use filepath for CDF path
Rgraphviz
graphviz 2.16 is not good
preprocessCore
(1.3.1) rma.background.correct() was not correctly returning value when copy ==TRUE
[/preprocessCore] permanent link
Biobase
I tried to fix the function addVigs2WinMenu so that it actually adds the
proper vignette title to the GUI menu and not the truncated filename!