[Bioc-devel] NEWS April 2007
jmacdon at med.umich.edu
Wed May 2 18:59:33 CEST 2007
Fixed chi-square calculation a bit to be actual counts in the
cells rather than the counts of the marginals in a couple of
Fixed bug in write.sgr when colnames were not defined on vals
Added 'cdf' argument to xy2indices() and indices2xy() so those
without an AffyBatch can still map things. The cdf argument in
this case is simply the name of the requisite cdf package.
Bugfix to vennSelect() when the number of probesets == 1
Fixed issue with non-square cel file parsing using binary (xda)
format cel files. The Affymetrix documentation is
inconsistent with the reality (rows, cols swapped).
Fixed GO links
Updated AnnBuilder to accommodate the changes to KEGG website.
Added support for Bos taurus and fixed parsing routine for
Fixed GO helper functions to deal with missing NA entries.
Use sample.ExpressionSet data for Pretty Output vignette
Changes to demo vignette to compare env and SQLite based
Add a revmap method for environment objects This allows revmap
to be used on environment-based ann pkgs
Added man pages for 'db_conn' and 'db_file' to HGU95AV2DB
Changed readBeadSummaryData to read BeadStudio V2 output
CreateBeadSummaryData now assigns array names to the columns
of the intensity data - 'pData' and 'phenoData' now defined
for BeadLevelList - added 'targets' argument to qcPlots and
updated man page
Bayesian integrated analysis of Affymetrix GeneChips
listLen now returns an integer vector (rather than numeric)
and I also tried to better the documentation
Further refinement of listLen In package code, INTEGER() is a
function, so it is better to call it only once. Also improved
the error message to give more information and added some
detail to the man page.
Add ScalarCharacter class This is a utility class that can be
used to ease validation burden when writing classes that
require a string slot.
Add assayDataElement<- function
Add readExpressionSet, deprecate read.exprSet, read.phenoData
Changed welcome message
This package provides examples and code that make use of
the different graph related packages produced by
Fixed listAttributes function
Removed array argument from getGene, getFeature and getGO as
affymetrix arrays can now be specified using the type argument
of these functions. Removed to.array and from.array arguments
from getHomolog function as the affy arrays can be specified
using the from.type and to.type arguments. To extend the
possible types of identifiers that can be used for the
getGene, getGO,etc functions, the value for the type argument
has to be a filter given by the listFilters function.
Updating handling of BooleanFilters. Whenever the user now
uses a boolean filter a value of 1 or 0 will have to be
specified to indicate true or false. To see if a filter is
boolean the user can run listFilters with the showType
argument = TRUE.
Slimmed the listDatasets function, and it now returns a
dataframe with character columns rather than factors
Added specification of the web server port. Two new BioMarts
don't use the default port 80 and were not accessible before
Rewrote XML parsers to make code cleaner. Added detection of
filter options. Some filters have a predetermed set of values
and now these can be shown using the filterOptions
function. Added the function filterType so users can determine
the type of a filter (is important to know which filters are
booleans). Updated vignette with the two new functions.
Replaced slots "start" (integer), "end" (integer) and "desc"
(character) by single slot "views" (data frame with cols
"start", "end" and "desc") in "BStringViews" class definition
Added the matchProbePair() function
Made matchProbePair() a new generic instead of a
function. Default for 'baseOnly' arg in alphabetFrequency()
is now FALSE instead of TRUE. Deprecated as.complex() in
favor of toComplex()
Changed median.polish.summarize.BufferedMatrix to
Expose makeChrBandGraph. This patch also fixes the root node
so that it does not contain all annotations.
Add chrBandInciMat and makeChrBandInciMat functions
Add geneIdsByCategory and doc
Move sigCategories to Category and make it a generic
Fix bug in hyperGTest for ChrMapHyperGParams objects R's
intersect(x, y) function returns a vector with mode matching y
if x and y have different modes. The bug was the result of
assuming that standard coerce rules apply. They don't in this
case as is documented in the intersect man page.
Fixed a bug in the read function (that didn't seem to have an
effect in previous R versions), and made the verbose output a
Small change in copaPerm() that speeds the operation by about
a gazillion-fold. Thanks to Laurent Gaultier for pointing this
Multivariate correlation estimation and statistical
inference. See package vignette.
Added code to not split if maximal statistic is small (<= 0.1)
and split if it is large (>= 7) without computing the
Added warning that windowing code wil be deprecated in version
Updated Subset for new multiple filter options. Also fixed
Big changes to HowTo vignette. * Minor changes to coercion and
read.flowSet to address Errol's troubles. * Removed as()<-. I
guess Seth will be happy. * Minor documentation changes * A
couple of small bugs with split * A $ accessor for flowSets
Updated GDS2eSet to return an object of class ExpressionSet
instead of the old exprSet
Fixup and document termGraph, inducedTermGraph, and
Fixed up the compGdist function a bit
Modification to probeSetSummary() to allow end users the
option of passing a vector of probeset IDs so the output of
this function actually counts _all_ probesets that contributed
to a significant GO term.
Fix subGraph attribute handling for graphNEL This needs to be
generalized for all subGraph methods. This patch adds proper
handling of node and edge attributes for the subGraph
operation. Before, we copied all attributes and now we only
copy over the appropriate subset.
Fix documentation of graphNEL class
addEdge for graphNEL warns if edge already exists Note that
for graphAM, this is an error. We warn when replacing an
already existing edge using addEdge because in the past some
users used graphNEL for representing non-simple graphs with
multi-edges. Since this is no longer supported, a warning
message is helpful.
limma 2.9.17 - bug fix to read.maimages() for
source="arrayvision". Now reads arrayvision files again for
the first time since version 2.3.1.
Modified make.cdf.packages() to create an additional
environment with the usual package name appended with 'dim'
(e.g., hgu95av2dim) that contains the chip dimensions. This is
intended to be used by indices2xy() and xy2indices() in the
affy package as a replacement for the deprecated xy2i() and
Bug in mfuzz.plot2 fixed
Added a svd method that is robust to outliers. Also a pca
method based on this robust svd.
Added vingette discussing handling of data with outliers
nipals(center=T) was also accidentially sclaing the data, as
we used scale(data, center=T). This has been fixed.
svnImpute returned too many scores/loadings, this was
fixed. And now we also assign correct row/column names to
Fixed bug in drawGate when adding additional regions
Most analyses of Affymetrix GeneChip data are based on
point estimates of expression levels and ignore the
uncertainty of such estimates. By propagating uncertainty
to downstream analyses we can improve results from
microarray analyses. For the first time, the puma package
makes a suite of uncertainty propagation methods available
to a general audience. puma also offers improvements in
terms of scope and speed of execution over previously
available uncertainty propagation methods. Included are
summarisation, differential expression detection,
clustering and PCA methods, together with useful plotting
and data manipulation functions.
Added movt() - a moving t-test method for reb()
rename LLagopen to agopenSimple
Provide more informative error messages when Java -> R data
tests go wrong
Add indexNA in RComplex and RNumeric, and modify convert
functions correspondingly. We tried to use NaN to represent
both NaN and NA for R complex and R numberic vectors in
Java. Now we seperate those two concepts. * change the java
class name that represents all functions in a package from
<package>.java to <package>Function.java
EBAM updated, added new vignette
Posterior probabilities are truncated at zero
Updated function segChrom and segmentation vignette
Modified findPeaks method: - Moved column "i" (peak number
within combined EIC) to the second-to-last column - Added
column "sn" with signal to noise ratio xcmsSets now include
"i" and "sn" columns in the peaks matrix
Added : - rawEIC method - findMZBoxes method -
findPeaks.centWave method Modified findPeaks() method to
support different findPeaks.* algorithms
Added some lines concerning findPeaks.centWave to the
vignette, changed output of centWave to matrix instead of
Removed formerly deprecated function clustunique() Changed
xcmsEIC plotting function from an S4 to an S3 method Removed
all instances of isGeneric()
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