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Bioconductor Changlog.
Tue, 13 Oct 2009
genefilter
update genefilter manual page to indicate form of user-supplied filters
genefilter
The distance computation in dist2 now has na.rm=TRUE.
genefilter
Reconciled nsFilter and varFilter when var.func = IQR.
genefilter
Removed methods for soon to be defunct exprSet class.
genefilter
Removed some accidental comments.
Just trying to be neat.
Make genefiltering work with yeast platforms.
This change should enable genefilter to work properly with yeast and
arabidopsis chip packages which each are based around a different
central ID than humans.
genefilter
The default argument of 'fun' now produces a metric (namely, L1 norm). It didn't before.
genefilter
I have tried to rationalize the interfaces of rowttests, colttests,
not all.
More importantly, the return result is now a data.frame, with row.names
that are taken from the corresponding dimension name of the input
matrix. The degrees of freedom (df) are now an attribute of the returned
object.
genefilter
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
genefilter
a change to remove the extern C piece around a header inclusion
thanks Martin
genefilter
I modified the code to use a numerically more stable one-pass algorithm
for the computation of the variances and means in the t-tests.
This is intended to cure the inaccurate or even wrong results that were
genefilter
some cosmetic surgery
genefilter
I updated the man page of nsFilter based on suggestions by Richard
Bourgon.
genefilter
fixed Rd version 2 parser warnings
genefilter
Swapped usage of old style deprecated annotation paradigm with new AnnotationDbi paradigm.
genefilter
taking characters as classifications now
genefilter
Put a fix in half.range.mode what data has length 0.
genefilter
added literature citation for introductory atrticle about ROC curves
genefilter
Fixed bug in rowpAUCs for very small values of p.
Also updated documentation
genefilter
Fixed bug in rowpAUCs for very small values of p.
Also updated documentation
genefilter
editing genefilter continued, some minor man edits
editing genefilter continued
editing genefilter per discussion w/Robert, Florian
genefilter
Minor Typo Fixes.
genefilter
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
genefilter
Added a caveat to the man page of rowttests regarding large group sizes.
genefilter
varFilter removes probes for which var.func returns NA, rather than
genefilter
Updated a reference in the man page (GS's new report)
genefilter
Removed an assumption from some mget() calls that results will never have missing values.
genefilter
I cleaned up the code comments.
genefilter
bumped up to 1.18
genefilter
Better error message from "shorth" if NA/NaN values are passed and na.rm
is not TRUE.
genefilter
Updating the license reference to reflect R standards.
genefilter
updated documentation to better explain the flipping of ROC curves
fixed typos in the documentation
auto-flipping is now an option in rowpAUCs and pAUC. The default is to flip
genefilter
Minor change to imports.
Bumping the version number.
Removed unneeded comma.
cleanup package dependencies
eanup package dependencies
genefilter
In function "dist2", the value of the diagonal elements of the returned
matrix can now be specified by the user, and the default value is 0.
Previously, NA was hard-coded.
genefilter
I fixed replaced
fun=function(a,b) mad(a-b)
in the dist2 function by
fun=function(a,b) median(abs(a-b))
This makes more sense.
genefilter
Changed biocViews entry of Statistics to Bioinformatics.
genefilter
Better discussion of type I error issues.
genefilter
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
genefilter
Added a note to the manpage of genefilter regarding unequal sample sizes and IQR