[BioC] Recent changes to Bioconductor packages

madman at jimmy.harvard.edu madman at jimmy.harvard.edu
Sat Feb 21 11:00:03 MET 2004

This is an automated message sent out weekly to report recent changes
to Bioconductor packages.  Please see the URL 
http://www.bioconductor.org/changelog.html for a complete history of 
changes.  Unless otherwise noted, these changes apply to the developmental
packages only.
21 Feb 2004: limma 1.5.1.
- now passes R cmd check for R >= 1.7.1 including R1.9.0dev
- removed package argument from calls to .C and .Fortran loess hooks in modreg
- edited package dependencies in DESCRIPTION file.
- dimnames and length methods for RGList, MAList and MArrayLM objects
- bug fix in duplicateCorrelation() which was not finding the M matrix when
  object was not an MArrayLM
- new argument 'resort.by' for toptable() and topTable()
- changes to loessFit() to avoid errors with small numbers of observations
- argument 'path' added to readSpotTypes() and readTargets()
- check in duplicateCorrelation() for correlation less than -1
- more expository comments added to 2.Classes.Rd
- duplicateCorrelation now uses randomizedBlockFit from the statmod package
  instead of gls from the nlme package.  This results in a several-fold
  increase in speed for duplicateCorrelation and dupcor.series.
- dupcor.series now deprecated
- getLayout() now has option to guess spacing between duplicate spots
- new function blockDiag() to form block diagonal matrices
- fix bug in imageplot() which caused overprinting of plots when using
- new function poolVar to Welch-style pooling of sample variances with
  unequal variances
- new functions usersguideURL() and .First.lib() to implement limma
  entry in Windows drop-down Vignettes menu
- bug fix for write.fit() (was failing when adjust p-values with
  multiple contrasts)
- updates to references as linear modelling paper now accepted for

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