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Bioconductor Changlog.
Mon, 15 Jun 2009
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
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.
limmaGUI
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
limma
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
limma
18 April 2009: limma 2.17.21
- basic (matrix-like) methods added for ElistRaw objects,
including cbind, rbind, subsetting etc.
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
13 April 2009: limma 2.17.19
- ebayes() now returns lods as a matrix. This ensures that
MArrayLM objects always be subsetted by column names, even
when there is only one column.
- new argument channels for read.maimages(), which allows the
function to read one-channel data.
- new class EListRaw for non-normalized one-channel data.
- printHead() now prints compactly for recursive lists of
arbitrary depth.
limma
Fixing minor typos.
limma
Bug fixes to the calculations of up, mixed and down p values in romer().
limma
Bug fixes to the calculations of up, mixed and down p values in romer().
Bug fixes to the calcualtions of p values in romer()
limma
Comment added to geneset.R.
limmaGUI
Added NAMESPACE file
limmaGUI
Added NAMESPACE file
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
- 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
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
- New function romer for rotation-mean50-rank version of GSEA (gene set enrichment analysis).
- New function symbols2indices which returns list of indices.
limma
Forgot to svn-add plotMDS.R to last commit.
limma
Forgot to svn-add plotMDS.R to last commit.
limma
23 March 2009: limma 2.17.13
- New class EList for one-channel microarray data.
- New function plotMDS(), which makes a multidimensional
scaling plot, using a particular distance measure.
limmaGUI
Changed biocViews entry of Statistics to Bioinformatics.
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.
limmaGUI
fixed Rdversion 2 parser warnings
limma
5 February 2009: limma 2.17.10
- update to backgroundCorrect help page to reflect published
papers.
- update to treat help page to reflect published paper.
- lmFit now looks for a design matrix in an MAList data object,
if one exists.
limma
19 Jan 2009: limma 2.17.9
- fix to a toptable() bug, which caused t-statistics to be out of
order when p<1 or lfc>0.
- color of the trend line drawn by plotSA() changed to red.
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.
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
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
4 Jan 2009: limma 2.17.4
- C code dynamic library is loaded when package is loaded
rather than when it is attached, to enable other packages
to import limma. (Not user visible)
- minor edits to geneSetTest and roast help files.
limma
4 Jan 2009: limma 2.17.4
- C code dynamic library is loaded when package is loaded
rather than when it is attached, to enable other packages
to import limma. (Not user visible)
- minor edits to geneSetTest and roast help files.
limmaGUI
Removed whitespaces from Rd files containing /items{stuff} {
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
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
22 October 2008: limma 2.17.1
- minor updates to the User's Guide
limmaGUI
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
limma
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
21 October 2008: limma 2.15.18
- refinements to barcodeplot() to make the graphic a bit prettier
limma
Comments added to barcodeplot.R code.
20 October 2008: limma 2.15.17
- new function barcodeplot(), which gives a graphical
representation of geneSetTest() using ranks.
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
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
28 Sept 2008: limma 2.15.13
- more efficient memory management in normexp.c (not user-visible)
- argument bg removed from internal functions .normexp.m2loglik,
.normexp.gm2loglik and .normexp.hm2loglik (not user-visible)