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Bioconductor Changlog.
Tue, 13 Oct 2009
limmaGUI
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
limmaGUI
Removed whitespaces from Rd files containing /items{stuff} {
limmaGUI
Added NAMESPACE file
limmaGUI
Added NAMESPACE file
limmaGUI
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
limmaGUI
Added GUI biocView to DESCRIPTION file.
limmaGUI
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
limmaGUI
fixed Rdversion 2 parser warnings
limmaGUI
change double dashes to single dash
changes on dashes to ordinary ones
limmaGUI
Changed biocViews entry of Statistics to Bioinformatics.
limma
Forgot to svn 'add' getEAWP.Rd previously.
limma
14 December 2007: limma 2.13.2
- update normalizeBetweenArrays(method="vsn") to reflect
changes in the vsn package version 3.4.1.
- additions to the help file for MArrayLM-class objects
limma
21 August 2008: limma 2.15.11
- new option "none" for the sort argument of topTable().
- new function roast() which does rotation gene set testing for
linear models.
- new function treat() which computes empirical Bayes moderated-t
p-values relative to a minimum required fold change threshold.
- new function removeBatchEffects() which removes batch effects
from microarray data.
- tableF() now gives a friendlier error message when the fitted
model object doesn't contain F-statistics.
limma
13 Jan 2009: limma 2.17.5
- paragraph added to details section of roast() help file
to explain simulation method used to estimate p-values.
limma
1 October 2008: limma 2.15.14
- minor improvements to several help files
- correction to the "bic" method of selectModel().
In limma 2.15.12 but not previously noted:
- new function selectModel() which implements Akaike Information
Criterion (AIC) or Bayesian Information Criterion model (BIC)
selection between alternative linear models.
limma
Replaced usage of soon to be defunct class exprSet with ExpressionSet.
limma
28 May 2009: limma 2.19.1
- Barnard (1963) reference added to roast.Rd.
- rewording of details in romer.Rd.
- two fixes to contrasts.fit() when there are non-estimable
coefficients in the linear model. The function previously
gave a warning about coercing double to logical, which no
longer appears. The function also failed in this situation
when the contrast was a single vector instead of a matrix.
- convergence criterion for arrayWeightsSimple() is now more
lenient for large data sets. About 5 decimal place accuracy
is still achieved.
- arrayWeightsSimple() now checks for failed convergence
from floating point errors and returns a diagnostic message.
- getEAWP() and lmFit() now return Amean values for EList
objects.
- calculation of rotation p-values in roast() and romer()
changed to be (x+1)/(nrot+1) instead of x/nrot, where x is
the number of random rotations giving a more extreme statistic
than that observed.
limma
18 April 2009: limma 2.17.21
- basic (matrix-like) methods added for ElistRaw objects,
including cbind, rbind, subsetting etc.
limma
Comment added to geneset.R.
limma
22 October 2008: limma 2.17.1
- minor updates to the User's Guide
limma
16 June 2008: limma 2.15.9
- new capabilities and arguments for write.fit(). The argument
method allows p-values to be adjusted globally instead of
separately, and the argument F.adjust allows the F-statistic
P-values to be adjusted.
limma
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
limma
20 March 2009: limma 2.17.12
- Bug fix to rowname assignment for MAList and RGList objects
containing matrices in 'other' component
- lmFit() warning message on NA coefficients is now more
refined. It now appears only when the coef vector is
partially NA for some probes.
- Fix to gls.series() so that it does not fail when the
weight matrix contains NA values.
Changed biocViews entry of Statistics to Bioinformatics.
limma
10 Nov 2008: limma 2.17.3
- fix to toptable() bug which caused an error when user
selected p<1 and lfc>0
limma
improved LaTeX citation
limma
11 June 2008: limma 2.15.8
- further bug fixes to getEAWP() when object is of PLMset class:
weights and Amean components were not being set.
limma
15 June 2009: limma 2.19.2
- new function topTreat() for listing top results by treat().
- treat() now outputs thresholded t-statistics.
- reference added to intraspotCorrelation.Rd.
- romer() now outputs the number of genes in each gene set.
- arrayWeights() now displays convergence info when TRACE=TRUE
for method="genebygene" (for every 1000th gene).
limma
23 October 2008: limma 2.17.2
- minor improvements to the help page for topTable and topTableF.
- bug fixes to the way that topTable() and topTableF() handle
sort="none".
limma
Cosmetic changes to printHead().
14 April 2009: limma 2.17.20
- bug fix to printHead() to handle object components which
are neither atomic nor recursive.
limma
Forgot to svn-add plotMDS.R to last commit.
limma
- Bug fix to the calculations of either and down p values in romer().
- Change function .meanTop() to .meanHalf() which gives means of top
half and bottom half of the ranks.
limma
Forgot to svn 'add' getEAWP.Rd previously.
limma
2 January 2008: limma 2.13.3
- Section on Mutiple Testing Across Contrasts added to the
User's Guide.
- The bibTeX entry returned by citatation("limma") now uses
@incollection styole instead of @inbook, thanks to Joern Toedling.
limma
Reversing changes committed in error to plots-ms.R on 9 March 2008.
limma
27 March 2009: limma 2.17.15
- further work on plotMDS() to make arguments and help
page clearer.
27 March 2009: limma 2.17.14
- New function romer() for rotation gene set enrichment analysis.
This can be viewed as a version of GSEA for linear models.
- New function symbols2indices() which matches a list of
gene sets as symbols against of vector of gene symbols.
- New function romer for rotation-mean50-rank version of GSEA (gene set enrichment analysis).
- New function symbols2indices which returns list of indices.
limma
15 Jan 2009: limma 2.17.8
- C code dynamic library is not unloaded when package
is unloaded. (Not user visible.)
- Some additions to alias2Symbol help page.
new argument expand.symbols added to alias2Symbol().
14 Jan 2009: limma 2.17.6
- new function plotSA(), which produces a "sigma vs A" plot for
a fitted microarray linear model.
limma
26 March 2008: limma 2.13.7
- the function rlm.series(), deprecated in 2004, is now removed
- add comments in the geneSetTest help file to warn that the
test assumes genewise independence.
limma
31 Aug 2009: limma 2.19.4
- bug fix to removeBatchEffect(), which gave incorrect
results when design=NULL.
limma
9 October 2008: limma 2.15.15
- the criterion for the "Active" column output by roast()
is changed to be more discriminating.
- new method "mallowscp" for selectModel().
limma
16 April 2008: limma 2.13.8
- bug fix to normalizeBetweenArrays(method="vsn"). When the
function was updated on 14 December 2007 to use vsnMatrix,
it had not been noticed that vsnMatrix returns log2 results
whereas the older vsn function returned loge results. The
results returned by normalizeBetweenArrays(method="vsn") are
again now log2, similar to before 14 December 2007.
- method option "neldermean" for normexp.fit() corrected
to "neldermead"
- deprecated function splitName() removed
- the help page for backgroundCorrect edited for improved
readability