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Bioconductor Changlog.
Mon, 15 Jun 2009
vsn
Improved wording.
Typo Fix
Added another plot to the vignette, on background correction.
I added another figure, with the graph of the glog function.
vsn
I fixed some of the man pages of S4 methods and classes, now that
there is stricter checking of their accordance with the code.
I also extended the discussion in Sections 6 (missing values) and 12
(shrinkage) of the vignette.
vsn
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
vsn
Removed unneeded geneplotter dependency.
vsn
Clarifications in justvsn man page, following suggestions from Robert.
De-activated the progress bar.
vsn
I removed calls to x11() from the vsn man page.
vsn
I fixed a FP arithmetic sloppiness that led to an NA in the
"cut"ting of the row numbers into 5 hmean strata.
vsn
Replaced undefined \asinh with asinh in an \eqn{...}.
I extended the vignette with a section on the calib="none" option.
vsn
More aggressive use of NAMESPACE. Now we only depend on Biobase, the rest is imported.
removed quotes from do.call
vsn
I have rerun the tests in vsn/inst/scripts and checked in a newer,
slightly updated version of the convergence2.pdf vignette.
This verifies that the recent change in the robustness part of
the vsn2 optimizer did not break anything.
vsn
Fixes to plotLikelihood.R and testmlest.R
I added an experimental new functionality of estmating the variance
stabilizing transformation parameter *without* the affine calibration
(i.e. assuming that calibration has already been done, e.g. using
quantile normalisation)
vsn
I made the Makefile in inst/doc a bit nicer.
vsn
I clarified the "Description" field.
vsn
I added a section to the vignette that describes normalisation with a
spike-in subset of features.
vsn
I reverted R/zzz.R back to how it was in revision 34609 (the changes
that Robert made)
vsn
Clarification of the explanation of the "subsample" parameter for the "AffyBatch" method of
"vsn2".
Fixed the formating of the welcome message / progress notification.
vsn
Needed to adapt how "normalize.AffyBatch.methods" is used to reflect a recent change in the affy package.
meanSdPlot now also returns px and py.
vsn
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
vsn
updating vsn to be in line with the new affy package
mostly cosmetic, but the affybatch.example data is gone
vsn
Clarified License Field.
vsn
Removed the handling of the "other" slot in "RGList", which seemed
error-prone and unnecessary. Now it is ignored, and a note is printed.
vsn
Removed the handling of the "other" slot in "RGList", which seemed
error-prone and unnecessary. Now it is ignored, and a note is printed.
vsn
Clarified the documentation of the (old) vsn and vsnh functions wrt the
point that they are superseded.
vsn
Better default value of the "subsample" argument of normalize.AffyBatch.vsn, following suggestion from Markus Schmidberger.
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.
vsn
I added a section to the vignette about the relationship between vsn
parameters and the additive-multiplicative error model.
vsn
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
vsn
Added lattice to the Depends field.
vsn
Fixed some wordings in a vignette.
vsn
Wee fix in formating of progress output.
The offset "hoffset" (called "c" in the vsn2 man page) is now computed
separately for each stratum, following a suggestion by Hans-Ulrich
Klein on the mailing list.
vsn
Replaced usage of newly defunct class phenoData with AnnotatedDataFrame.
vsn
Removed support for soon to be defunct class exprSet.
vsn
Fixed Typo
Better handling of cases when options "subsample" and "reference" are used in combination.
A friendlier message for users of 'vsn' (i.e. the predecessor of
'vsn2').
vsn
added Newline.
vsn
Fixed man page description of "siqsq" slot after email from Leo J Lee.
vsn
Disabled the option to call vsn reference with the subsample option.
Need to fix it.
Some better messages, and fixed a BUG that affected the case when vsn2
was called with a "reference" argument, and if that reference argument
had been produced by a prior call to vsn2 in which "subsample" was set.
Fixed a bug in vsn2: hoffset slot was not calculated
if (returnData==FALSE); now it is always calculated.
vsn
Three changes:
1. The function "meanSdPlot" now returns the midpoints and values of the
moving median smoother of the standard deviation vs mean (or rank of
mean) function. There is also a new function argument 'plot' whose
default emulates previous behaviour, but when set to FALSE the plot is
not made.
2. The deprecation message of the 'old' vsn now a bit friendlier.
3. I suppressed printing a cryptic warning message from the numeric
likelihood optimisation.
vsn
I have improved some of the wordings in the "Reference Normalization"
section of the vignette.
vsn
I added checking whether the input data contain NaN.