[Bioc-devel] NEWS - July 2007

James MacDonald jmacdon at med.umich.edu
Sun Aug 12 04:01:52 CEST 2007

	July 2007


	  Removed R_affx_cdf_deprecated.cpp, wasn't need and it gave
	  errors on R-2.6.0 due to CHAR changes

	  Optimized writeCdfHeader() for memory. For a CDF with
	  1,200,000+ units just writing the unit names would consume
	  1-1.5GB RAM. Now it writes unit names in chunks keeping the
	  memory overhead around 100-200MB.  o Made convertCdf() more
	  memory efficient.  o BUG FIX: The error message in
	  isCelFile() when the file was not found was broken.  o
	  Updated to v1.9.2 on BioC devel.
	  Version: 1.8.1 [2007-07-26] o Now affxparser install on OSX
	  with PPC.
	  Version: 1.7.6 [2007-03-28] (never committed until v1.9.2) o
	  Modified findCdf() such that it is possible to set an
	  alternative function for how CDFs are located.


	  Yeast ORF IDs were being processed using a logically flawed
	  mechanism which sometimes would toss out part of the
	  ID. This is now fixed.

	  Seth noticed some bad looking bugs, which I have fixed here
	  and then tested to make sure that the code was not dependent
	  on any of these bugs to run...


	  Added lines for new Agilent and GO pkgs.
	  I believe that this adds the rest of the supported rat,
	  mouse and human Agilent packages. Next I will add other
	  I also updated the line/db for the modified GO.sqlite
	  db. This GO.sqlite file is now an order of magnitude smaller
	  than it was before.

	  Added paths for arabidopsis builds.
	  These appeared to be partially finished. So I
	  have added code to finish the sqlite portion.
	  Since they are avaialable now, I have added them

	  schema. Version bump.

	  pkg template names now have the ".DB" suffix instead of just

	  A few more edits needed on the GO.DB man pages (only
	  strictly required edits for now, these man pages will really
	  need to be revisited at some point...)

	  started fixing createAnnObjs.YEAST2_DB()

	  Finished fixing createAnnObjs.YEAST2_DB(). Version bump.

	  added a "Proposal for schema improvements" section

	  Fixed createAnnObjs.AG_DB(). Version bump

	  added pkg template for KEGG + a new entry in the master
	  index file (inst/extdata/ANNDBPKG-INDEX.TXT)

	  Added missing packages.
	  Added many new packages for custom arrays.  Wherever
	  possible, these packages have also been labeled for

	  some rearrangement to the master index file

	  Added support for the KEGG_DB schema. Version bump.

	  chipName entry not needed for Qiagen chip

	  Fixed createAnnObjs.YEAST_DB(). Version bump.

	  more polishing to the YEAST_DB section

	  createAnnObjs.YEAST_DB() so now the COMMON2SYSTEMATIC map
	  uses the right table.

	  Fixed the ENZYME and ENZYME2PROBE maps for AG_DB
	  schema. Version bump.

	  Added missing ACCNUM map for AG_DB schema.

	  Added the YEAST2.DB pkg template for YEAST_DB-based pkgs
	  (annotations for yeast chips). Version bump

	  Added the AG.DB pkg template for AG_DB-based pkgs
	  (annotations for Arabidopsis chips). Version bump.

	  Changed package names. New files are also rdy.
	  To coincide with changing all the pkg names, I have also
	  pushed over pkgs that *have* the new names in them so that
	  things should hopefully line up without incident.
	  Propagated new db schema names all over the
	  place. Reorganized the master index file. Version bump.

	  Added support for new RODENTCHIP_DB schema.

	  Added the species field for each species-based pkg to the
	  master index.

	  Added support for new HUMAN_DB and RODENT_DB
	  schemas. Version bump.

	  Some adjustments to the reverse maps created by
	  createAnnObjs.HUMAN_DB() and createAnnObjs.RODENT_DB().

	  PFAM and PROSITE maps (IpiAnnDbMap objects) are not
	  Added man pages to the KEGG.DB template (taken and adapted
	  from AnnBuilder).

	  Forgot to put the man page for the MAPCOUNTS map in the
	  KEGG.DB template (this page is inaccurate and will need to
	  be fixed in _all_ templates).

	  Forgot to put the man pages for "db_conn" and "db_file" in
	  the KEGG.DB template. Fixed example for "db_conn" man page
	  in the GO.DB template.

	  One more thing to do when we rework our DB schemas.

	  Changed expected name of the eg map files.
	  Just changed the expected name of the eg mapping files to
	  match what is being now produced by the pipeline...


	  Work on NChannelSet, have to fix the problem with default
	  "numberofgraphs" and "on" for AffyBatch.

	  problem of "con" and "numberofgraphs" fixed

	  problem with "man" fixed

	  Modifications on the way of splitting the density plots and
	  on the option to log transform the data.

	  Mix between boxplots and density plots figure numbers and
	  legends fixed.

	  outfile argument is now named prefix

	  subdirectory issues solved, add spatial effect plot for

	  Add an index in the beginning of the report.  Add the qcstat
	  plot from simpleaffy.  Add precisions in the help and the

	  Small modifications on the background and foreground

	  modified the file handling code


	  getArrayData() can return log-ratios ("M"), average
	  log-intensities ("A") or residuals ("residR") or ("residG")
	  by changing the which argument.  - plotting functions
	  (boxplotBeads, imageplot) able to plot bead residuals,
	  log-ratios or ave log-ratios - new function beadResids()
	  calculates residuals for each bead on an array.  -
	  readIllumina() gives more meaninful warning messages when no
	  files are found. - readIlumina(): default textType argument
	  changed from ".csv" to ".txt"

	  new function readBGX() to read in Illumina's .bgx files for
	  expression BeadArrays - fixed typo in readIllumina()

	  fixed typo in readBGX.Rd file

	  createBeadSummaryData() modified to handle version 2
	  BeadChips with 2 strips per array. Human 6 arrays have all
	  the beads spread across 2 strips for Human6, rather than
	  different beads on each strip as per version 1.  - bug
	  fixes: beadResids() and getArrayData() - removed extra
	  bracket in boxplotBeads.Rd documentation

	  modified C code for findBeadStatus to handle case when mad=0

	  normaliseIllumina, offers normalisation for ExpressionSetIllumina
	  - readBeadSummaryData, default options changed to handle
	  BeadStudio 3 output (skip=8, added 'quote=""' to read.table
	  (default 'quote'
	  caused R to hang for some BeadStudio version 3 output))
	  sep arguments to be correct for version 3 outputetc.)
	  - vsn2 used in normalizeSingleArray, instead of vsn
	  - displayTIFFImage and plotCoord removed
	  - plotMA and plotXY updated to now check for and exclude missing
	  values from plotting
	  - createBeadSummaryData now checks that the arrays it combines
	  (when 'imagesPerArray=2') are the right ones. New argument
	  'what', which allows log-ratios (M), average intensites (A), red
	  (R), green (G) or red and green (RG) intensities to be
	  summarised. Default 'imagesPerArray' set to 1 instead of 2.
	  - getArrayData: typos in error messages fixed. New 'which' option
	  top get residuls from log-ratios.
	  - readIllumina: default background correction option changed to
	  - imageplot: changed default nrow and ncol to 100 (was 18 and 2
	  - beadResids() simplified after changes to getArrayData
	  - updated man pages


	  lost serial argument to bgx - not very useful

	  Changed IACT and MCSE to muiact and mumcse

	  changed a cat() to warning(), renamed basepath to rundir,
	  renamed dirname to inputdir, changed default rundir to
	  . instead of inside tempdir() to avoid losing valuable runs
	  on R quit
	  cleanup + fixed bug where thought i was using 0-indexed var
	  instead of 1-indexed var. all C code is 0-indexed now

	  Fixed bug with normgenes parameter to analysis functions


	  Additional accessors for eSet
	  * fData, fvarMetadata, fvarLabels access underlying data,
	  varMetadata, and varLabels for featureData
	  * Remove duplicated documentation and code of varMetadata
	  * Minor tweak to remove "[1]" from eSet 'show'

	  Harmonize dimnames of ExpressionSet assayData elements, if
	  * 'harmonize' means to ensure that all dimnames are
	  consistent with names from phenoData, featureData
	  * Only possible if elements differ with NULL dimnames, not
	  if elements have different dimnames; in this case, signal an
	  error about conflicting dimnames

	  selectChannels was not copying all appropriate data
	  Documentation tidy on ExpressionSet

	  Fix bug in combine method when no rows are shared
	  Thanks to Laurent Gautier for the bug report and patch.

	  Revised patch on combine data.frame's
	  Row.names can be stored as integer, but 'merge' reports them
	  as character; force to integer if both incoming data frames
	  have integer row names.
	  Added comment to (reverted) switch(), where ordered=,BLAH
	  applies identity requirement BLAH both to ordered factors
	  and as default (for non-factors).
	  Revised unit test name to reflect underlying issue.

	  More lenient contraints to 'combine' data frames
	  Change 'identical' to 'all.equal(...,
	  check.attributes=FALSE)' so that row names on incoming data
	  frames can be stored differently (e.g., as character and

	  fixups and improvements to peek


	  Fixed getFeature function when using MySQL and the query
	  contains a chromosome name; Fixed error in Rnw file that was
	  caused by renaming of an attribute group in the Ensembl


	  Pattern size limit bumped from 10000 to 20000 letters for
	  Boyer-Moore. Version bump.

	  Added new BStringPartialMatches class. No version bump.

	  Added the "lcprefix", "lcsuffix" and "lcsubstr" new generics
	  (methods not implemented yet). No version bump.

	  Implemented "lcprefix", "lcsuffix" and added
	  "pmatchPattern". No version bummp yet.

	  Reimplemented "lcprefix" and "lcsuffix" in C (this boosts
	  "pmatchPattern").  Version bump.

	  use _Biostrings_ prefix instead of Biostrings_ for C visible
	  symbols that are not .Call entry points

	  started using Biostrings_ prefix for all .Call entry points

	  Revisited the match reporting mechanism shared by the
	  various matching algos
	  More refactoring of the match reporting mechanism.

	  Added a C routine for normalizing the views of a
	  BStringViews object and used it to boost the "masking a
	  BString object by content" operation.

	  Made matchPattern() and countPattern() work on a
	  BStringViews subject.  Added some examples to matchPattern()
	  doc. Version bump.

	  Got rid of some [TODO]s in the documentation.

	  added some examples

	  - Replaced internal helper function isLooseNumeric() by
	  isNumericOrNAs() with better semantic.

	   - Improved the "letter" generic and documented it.

	   - Got rid of some TODOs in BStringViews-constructors.Rd.


	  Improved examples in man/BSgenome-class.Rd. Version bump.

	  reworked the slots of the "BSgenome" class in order to
	  provide more information about the provenance of the genome

	   Added missing accessor methods for the "BSgenome"
	  class. All BSgenome slots can now be accessed (read only)
	  via a dedicated accessor method.  Documented these new


	  adjust how ties are handled.


	  Deprecate condGeneIdUniverse, add 'cond' arg to
	  geneIdUniverse now does the right thing given a result
	  object; that is, a conditional gene ID univ. is returned for
	  the results from a conditional test. There is an new
	  argument, cond, which defaults to TRUE. When called on a
	  non-conditional result, cond is ignored.

	  giving min.expected=NULL prevents column removal in


	  na.rm set to TRUE when finding qunatile values for
	  overlapping segements

	  Bug fix to remove duplicated mcrs in the output.


	  Added: feature extraction -- hull, texture (Haralick), edge
	  features. Corrected: tile rewritten in C, hundreds times
	  faster; stackObjects got 'rotate' argument to allow for
	  rotational alignment of objects while stacking. Multiple bug
	  fixes. New recompiled DLL. Hopefully corrected encoding in
	  moments.Rd (that BioC check was complaining about)

	  Done extraction of features: moments, hull, Haralick, edge,
	  Zernike moments! All new bug fixes.

	  optimized Zernike code, 6 times faster on N = 12

	  Completed a full set of feature extraction routines (still
	  new might be added in the future), for images with zero
	  objects matrices are returned instead of NULL, updated man
	  pages for feature extraction routines, optimized
	  performance. New dll

	  R CMD check bug fix (missing link + possibly uninitialized
	  value in C -- was Ok)

	  minor bug fix in stackObjects: failed if there was 1 single
	  object because subsetting generated a vector from a matrix
	  that did not have dims

	  different bug fixes in feature extraction, small bugs mostly
	  concerning images with no objects or 1 object only

	  manual 'ext' selection in 'stackObjects', 'combine' on a

	  more options in stackObjects: added index to stack only
	  selected objects

	  updated Windows DLL for the Windows build that takes into
	  account all recent changes in the C code

	  background reset to black on image 'rotate', need to
	  provide mechanism for specifying the background in future

	  workaround in man pages for bug in 2.6 rev 42284, result
	  should be
	  > a <- Image(0, c(2,2))
	  > class(a+a) [1]

	  bug fixes in write.image: quality and file names

	  small bug fix in 'image' correcting wrong aspect ratio

	  Zernike pseudo moments; added Arith methods to comply with


	  added rat database handling code

	  added exons.in.range and transcripts.in.range and did a bit
	  of code refactoring

	  updated plot functions to allow line type to be specified

	  better representation for exons with missing data in

	  specify lty for exon edges


	  New Package:

	      explore and analyze *omics data with R and GGobi


		Michael Lawrence


	  Untested fixes for NA testing of doubles
	  When testing whether a double value is NA, use ISNA()
	  instead of equality testing against NA_REAL. At least on
	  some platforms, the equality test will not work. This is
	  only an issue for doubles.


	  Modified filter constructors to accept parentId.

	  added a slightly friendlier error message


	  Extract parentId's from gatingML gates and store them in
	  parentId of filter objects.

	  Added a resolveParents function that combines related
	  (parent-child) gates for a given list of gates.

	  added compensation examples as a prelude to implementation
	  of code to read them

	  a start on parsing compensation ML


	  I copied the code for drawing rectangleGate and adapted it
	  to polytopeGate.


	  Fixed bug in rowpAUCs that lead to subtle inaccuracies of
	  the pAUCs

	  fixed a bug that was triggered on 64 bit machines


	  updated the data set, fixed a few bugs in man pages and
	  removed/updated code

	  Require R 2.5.0 and recent version of Biobase


	  Fixed a bug with 'xlim', 'ylim' in smoothScatter: they are
	  now also propagated to the 'image' function


	  (1) added Armitage.R and Armitage.Rd to test linear trend;
	  included the phrase 'Armitage.R' to the file 'DESCRIPTION';
	  added function names 'Armitage', 'Armitage.default',
	  'ArmitageTest', 'genotypeCoding', 'genotypeCoding.default'
	  to the file 'NAM ESPACE'.

	  (2) fixed two bugs in 'convert.cpp' which caused error and
	  warning messages when using Rdev to compile GeneticsBase.
	  The first bug is the unused variable 'maxlen'. The second
	  bug is caused by recent changes in R related to CHARSXPs.


	  plot_EvG modified to have better x axis


	  fixed bug in plot functions


	  put in some code for leaves etc

	  did the inEdges thing


	  more shell-like runfile.sh in unit test

	  Facilitate use
	  * setName, setIdentifier no longer required; use NA as
	  * default NullCollection rather than AdHocCollection

	  Correctly copy setName, rather than setIdentifier, when
	  duplicating object

	  Add GOCollection functionality

	  - GeneSet(GOCollection(ids, evidenceCode=codes)) consults GO
	  for appropriate EntrezIds
	  - Also bug fixes in mapIdentifiers

	  toBroadSet bug fixes
	  - Insist on BroadCollection
	  - use accessor for BroadCollection
	  - use con=stdout() as default connection

	  Bug fixes
	  - GOCollection error message
	  - GeneColorSet construtor guessing phenotypes better
	  - GeneSet show method

	  Added vignette sketch
	  - Documentation tidy (incomplete) on GOCollection

	  Quieten mapIdentifiers, geneIdType<-
	  * added verbose option
	  Additional cleanup
	  * use "*.db" for AnnotationDbi packages

	  * setIdentifier=.uniqueIdentifier() as default for

	  Generalize accessor construction methods to accept 'where'


	  modified functions to be less verbose, and modified silcheck
	  and msscheck to have more similar arguments


	  22 July 2007: limma 2.11.9
	  - improvements to the numeric computations of
	  dnormexp.saddle(), which is used by

	  - new function normexp.m2loglik.saddle(), which is the same
	  as normexp.m2loglik() but using the saddle-point
	  approximation.  - normexp.fit() has a new argument 'methods'
	  - default for n.pts in normexp.fit() changed to NULL,
	  meaning use all the points. The rule used to choose the
	  quantiles if n.pts is improved to give more nearly unbiased
	  parameter estimators.
	  9 July 2007: limma 2.11.8
	  - contrasts.fit() now warns if row names of contrast matrix
	  don't match column names of contrasts.

	  - plotMA3by2 has a new argument 'device' to specify the
	  graphic format.


	  Added new importance measures.  Changed logic.fs to logicFS,
	  and logic.vim to vim.logicFS.  New vignette will follow
	  after another major update.


	  Add the correction of the STDEV column values of the
	  BeadStudio output file (transfer the standard error of the
	  mean as the standard deviation)


	  Mfuzz option added to see.genes


	   Fixed bug in getProbeDataAffy, and converted 'what' list to
	  contain integers and characters instead of 'numeric' and
	  'character', which doesn't do anything.

	  Add revcompDNA and revcompRNA functions
	  These are implemented in C and return the reverse complement
	  for a given RNA or DNA sequence.

	  Add countbases
	  countbases returns a matrix of base counts and works for
	  either DNA or RNA based on the 'dna' argument.


	  adding predicted accuracy to crlmm

	  controlling memory usage


	  Major restyling of oneChannelGUI:

	  Reorganization of functions in the available menus.  Loading
	  of exon .CEL files, via APT tools, is now free of bugs.
	  DABG p-value calculation is now possible via APT tools.
	  MiDAS alternative splicing p-value calculation and filtering
	  are now free of bugs.

	  Loading of GEO Matrix Series files is now possible.
	  RanKProd methods were graphically interfaced.  Adding
	  annotation for gene-level core exon data, this will remain
	  until Bioconductor annotation libs willbe available Major
	  revision of oneChannelGUI vignette, an annotaiton vignette
	  was added

	  Massive error polishing. Vignette update.

	  Updating vignette.

	  Improving error messages Fixing some bugs in the
	  classification and filtering menu

	  Exon data analysis: Splice Index is now calculated using APT
	  tools together with MiDAS p-values, since it very efficient.
	  Rank product method (RankProd package) was adapted for the
	  identification of alternative splicing events.  Filters
	  based on MiDAS and rank product methods were implemented to
	  allow the selection of top ranking alterna tive splicing
	  events.  Adding two modules for metha analysis: merging up
	  to 3 data set to the data loaden on oneChannelGUI in
	  NormalizedAffyData evaluation of the itegrative correletion
	  coefficient as implemented in metaArray package.


	  Fix type errors in the mannul files


	  Check for valid paths at start of makePdInfoPackage

	  Rework runfile.sh for more shell-like script

	  minor bugfix in makePdInfoPackage-methods, createPackage
	  call used ... inappropriately

	  minor change to add biocViews as a constant in template
	  DESCRIPTION. should propagate from seed but didn't see
	  immediately how to do that

	  minor failure in size:k:enz string construction fixed

	  took out Rdev as default R command, replaced with R

	  Adding prototype for SNP6 platform


	  I have fixed a bug in the code...should not be dividing by 2

	  I have modified genBPGraph either to return a directed or
	  undirected graph now


	  fixed bug in batch import of multiple FCS files

	  fixed bug in subsetting of cytoSets


	  fix very minor ties issue. Also note that current functions
	  do not handle matrices with NA values (to be fixed in the

	  a little more code cleaning

	  now handle NA values. Also how the quantiles are estimated
	  when data is missing or target length differs from matrix
	  dimensions has been altered.


	  DEResult - new class. Using for results of a differential
	  expression analysis. Has methods show, statistic, FC,
	  statisticDescription, DEMethod, pLikeValues, topGenes,
	  topGeneIDs, numberOfProbesets, numberOfGenes, numberOfContrasts
	  and write.reslts.
	  mgmos, mmgmos, justmgMOS and just mmgMOS - bugfix and changed
	  defaults. Will now create an exprReslt object. gsnorm parameter
	  now has median as default, i.e. median-scaling normalisation will
	  be applied. Use none to specify no normalisation.
	  mmgmos - new input parameter. New input parameter addConstant is
	  an experimental feature. Using the default value gives identical
	  results to previous version of mmgmos.
	  pumaDE - changed return value. Now returns an object of class
	  calculateLimma - changed return value. Now returns an object of
	  class DEResult
	  calculateFC - new function. Calculates differentially expressed
	  genes using fold change.
	  calculateTtest - new function. Calculates differentially
	  expressed genes using standard t-tests.
	  calcAUC - new function. Calculates area under an ROC curve
	  numFP - new function. Calculates number of false positives for a
	  given proportion of true positives
	  removeUninformativeFactors - new function. Remove uninformative
	  factors from the phenotype data of an ExpressionSet.
	  createDesignMatrix - various changes. Now removes uninformative
	  factors, ensures there is at least one factor. Can now handle
	  ExpressionSetIllumina objects.
	  createContrastMatrix - various changes. Now removes uninformative
	  factors. Can now handle ExpressionSetIllumina objects. Now also
	  creates X_vs_other contrasts for factors with 3 or more levels,
	  in addition to previous contrasts created.
	  pumaPlots - bugfix. Replaced die() with stop()
	  plotROC - new arguments. includedProbesets, yaxisStat, xaxisStat,
	  downsampling, showLegend, showAUC
	  plot.pumaPCARes - newplot.pumaPCARes - newplot.pumaPCARes -
	  newplot.pumaPCARes - newplot.pumaPCARes - newplmb - various
	  changes. New parameter cl for a snow package cluster object. Can
	  now handle ExpressionSetIllumina objects. No longer relies on
	  se.exprs method. Noplot.pumaPCARes - newplot.pumaPCARes -
	  newplot.pumaPCARes - newplot.pumaPCARes - newplot.pumaPCAR
	  Ensures there is at least one factor.
	  pumaPCARes - removed plot method. This is now handled by
	  zzz.R - change to library.dynam call. zzz.R - change to
	  library.dynam call. zzz.R - change to library.dynam call. zzz.R -
	  change to library.dynam call. zzz.R - change to library.dynam
	  call. zzz.R - change to library.dynam call. zzz.R - change to
	  library.dynam call. zzz.R -ameter sorted to indicate whether
	  results returned should be sorted by PPLR or not. Also now
	  calculates means of different conditions rather than sums, to
	  account for unbalanced natures of 1 vs others contrasts.
	  Vignette updated to use DEResult class and methods, and includes
	  details of 1 vs others contrasts.


	  Added quantsmooth.seg for analysis of long sequences


	  New Package:

	      Some simple docbook support, principally in Xweave


	       Vince Carey


	  added a script for visualizing enrichment-transcript
	  relations as a graph using Rgraphviz and pointed to that
	  script in man pages

	  added one new visualization type (plus one minor variation
	  thereof) for chipAlongChrom

	  added a small convenience script for generating a targets
	  text file from the file SampleKey.txt provided by NimbleGen


	  * change the structure of interactors matrix: remove column
	  "IntAct ID" and use "IntAct ID" as row names

	  * use "IntAct ID" to reference interactors in the
	  interaction (or complex) list; "UniProt ID" is used

	  * improve the extraction of "IntAct ID": only consider
	  "secondaryRef" element before, now consider "primaryRef" as

	  improve the show method

	  I have added a vignette which will double for the supp mat
	  of the paper.

	  I have updated the SuppMat.Rnw file

	  I have made some minor modifications to the code as well as
	  the beginnings of a new function

	  I have written a new function to take XML files and generate
	  graph objects

	  I have fixed a bug in the vignette

	  I have updated the parser and added a new function

	  I have fixed a bug in list2Matrix

	  I have updated the package so that intactGraph and
	  intachHyperGraph are superclasses to graphNEL and hypergraph

	  I have updated the parser functions


	  New Package:

	      A package for refdb-based bibliography management


	      Vince Carey


	  I have moved list2Matrix to Rintact and changed the


	  Added findDelta, a function for computing the number of
	  genes called differentially expressed for a given FDR, and
	  vice versa.

	  Freedom for chisqClass and qvalue.cal. Necessary because of
	  upcoming changes in package logicFS.

	  Now a better version of the fold change is available (see
	  use.dm). However, old version is still default.

	  New Package:

	     Functions and classes for DNA copy number profiling of
              array-CGH data


	     Robin Andersson


	  deleted a few commented lines in AllClasses.R

	  removed fData and fData<- methods as these are now in
	  Biobase. allowed x.axis to be suppressed by argument xaxt=n
	  in plotSnp

	  removed fData help file

	  changed generic for plotSnp

	  removed generic definitions for fData

	  corrected unmatched braces in help files chromosome and

	  added useLayout argument to plotSnp

	  added two arguments to plotCytoband: outer and cytobandAxis

	  move packages in Depends to Suggests, updated show methods

	  changed copyNumber method for SnpQSets to

	  applied a bugfix patch from James Bullard


	  New Package:

	      Variational Bayesian Multinomial Probit Regression with
     	      Gaussian Process Priors. (Neural Computation 18,
     	      1790-1817 (2006))


	      Nicola Lama


	  much improved vignette "incremental.Rnw"

	  some updates to the write up

	  Now the optimisation is done with respect to parameters a,b:
	  h(x) = as inh((x+a)/b) instead of h(x) = asinh(a+b*x) as in
	  vsn 1.X and 2.X. I hope that this will better the
	  performance in cases where the multiplicative error
	  dominates over the additive.
	  Also the vignette "incremental.Rnw" with the likelihood
	  combinations is now much more detailed.

	  Fixed some bugs and typos so now the package passes R CMD
	  check and the vignette looks OK.

	  Generalized the vignette to a new and better

	  Oh boy, lot's of changes.  The optimisation is now done for
	  the parametrisation f(b)*x+a, and f() can be chosen quite
	  freely. Still needs to be tested more.

	  added the function scalingFactorTransformation

	  The "test" scripts now all work satisfactorily.  Still need
	  to update the vignette and convergence2.Rnw

	  I have updated the vignette to reflect latest changes

	  Updated sagmbSimulateData - is now a bit less extreme.

	  Now it passes R CMD check: Fixed man pages to reflect recent
	  changes in parameter names and semantics.  Now no longer
	  depend on limma (but use RGList via Namespace)

	  started adding justvsn method for NChannelSet. Not done
	  yet. Hope to continue tonight from home.

	  Added a justvsn method for NChannelSet.


	  Increased buffer size to 100000 in findMZBoxes() to handle
	  also files with a vast number of peaks

	  Fixed bug in MSW.getRidge() to catch empty ridgeLists

	  - The scale on which the peak was localised is also returned
	  - additional logical argument fitgauss, gaussian fits are no
	  - longer mandatory

	  - Integration method can be choosen: descent on the mexican
	  hat filtered data or on the real data. Method 2 is honest,
	  while method 1 (default) is more robust to noise .  - runs
	  much faster
James W. MacDonald, MS
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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