[Bioc-devel] NEWS

James MacDonald jmacdon at med.umich.edu
Tue Jul 24 03:55:46 CEST 2007

	July 2007


	  ReadAffy constructs AnnotatedDataFrame rather than calling
	  read.AnnotatedDataFrame; minor doc fixes


	   fix an issue in read_bpmap with SET_VECTOR_ELT()


	   References to Digestion changed to Degradation. Changed
	   Menu Item name and function names. See Bioconductor emails
	   from Gordon Smyth/Robert Gentleman around December
	   6th. 2006.

	   Fixed a bug in Normalize.R introduced in 1.10.1 - bracket
	   misplaced as shown below: Replaced this line
	   sep="\t",quote=FALSE,col.names=NA) with

	   Error on console when HTML report was to be created. It
	   read: "Error in get(x, envir, mode, inherits) : variable
	   "HTMLenv" was not found" Modify htmlreport.R replace:
	   try(assign(".HTML.graph", TRUE, env = get("HTMLenv", envir =
	   .GlobalEnv))) with: if
	   try(assign(".HTML.graph", TRUE, env = get("HTMLenv", envir =
	   .GlobalEnv))) }#end of if


	   replaced hgu95av2db by hgu95av2.db

	   Fix ann pkg detection for name change in SQLite-based packages


	   Updates for SQLite-based package rename db => .db


  	   Fixed broken example in ?GONode.

	   The rightColType slot for ENTREZID map is not set to
	   "integer" anymore (this slot should probably go away for
	   AnnDbMap objects since it seems that left names and right
	   names should always be strings if we want revmap() and the
	   upcoming "plug map" feature to work properly and in a
	   consistent manner)

	   Replaced "db" suffix by ".db" in all db package names. Small
	   improvements to makeAnnDbPkg()

	   Added experimental agilent package.
	   Package should look a lot like an hgu95av2.
	   This is because its using a similar set of
	   operations to knit everything together as
	   is used by that package. So it *should* work
	   as one of these.

	   Fixed bug in dbCountUniqueMappedVals(). Added debug.sql().

	   Added loadAnnDbPkgIndex() and use it in
	   "makeAnnDbPkg-character" method. Reorganized


	   backgroundCorrect() function now checks if background
	   correction has already been carried out before doing any
	   further adjustment - imageplot() now allows negative values
	   to be displayed (previously only plotted non-negative
	   values). Also gives a warning when NA/Inf values are
	   present. These are values are replaced with zeros - bug in
	   readIllumina() which meant background correction was not
	   taking place when useImages=FALSE now fixed

	   plotDERank now returns a matrix.


	   Add assayData documentation to ExpressionSet - reference
	   eSet, where info on subsetting also provided - add [[
	   documentation for AssayData

	   added "strbreak" to the show method for AnnotatedDataFrame

	   Provide more consistent AnnotatedDataFrame dimLabels for

	   Completed C-implementation of the Needleman-Wunsch algo
	   (src/align_needwunsQS.c). Depending on the size of the
	   strings to align, the new needwunsQS() function is 100 to
	   1000 times faster than the old one (pure R). Also, now
	   needwunsQS() returns a BStringAlign object (new class which
	   purpose is to describe an alignment between 2
	   strings). Deprecated alignScore() in favor of score(). Still
	   need to update needwunsQS() man page and to document new
	   BStringAlign-related methods (initialize, align1, align2,
	   score, show).

	   added nucleotide alignment example in needwunsQS() man page

	   added the complementViews() function + a split() method for
	   BString objects (will probably use another name for the
	   latter since there is some uglyness associated to the use of
	   the split() generic)

	   Renamed "complementViews" -> "mask" + mask() is now a
	   generic with methods for BString and BStringViews
	   objects. Some other minor (internal) changes.


	   add MoveStorageDirectory()


	   Use exact=TRUE in calls to [[ This resolves undesired partial
	   matching that was occuring in addChrBandAnnotation.

	   Fix gseaperm to work properly in absence of the Matrix


	   The function "normalizedChannels" was restored to the
	   behaviour it had before May 2007, and a new function called
	   "summarizeChannels" was added.  The "path" argument similar
	   to that in function "readPlateData" was added to the
	   functions "configure" and "annotate".  In "writeReport", the
	   option to add the tooltips to the image plot was set by
	   default to FALSE.

	   Corrected for the case where there are different batches
	   using different positive controls.


	   A completely revised (from scratch) implementation of cellHTS
	   To avoid too many tears from existing users, we give it a
	   new name, so they know they are in for some changes when
	   they install it.  Eventually, cellHTS can be taken out of
	   the releases.


	   bug correction in moments for the case when image does not
	   contain any objects


	   fixed a bug in checkMarkers so that allele frequencies can
	   be calculated correctly.

	   added 'drop=FALSE' for some R code to avoid converting
	   matrix to vector.

	   added a argument 'missingOutput' to the functions
	   'pedAFreq' and 'pedGFreq' to fix a bug that caused wrong
	   output of the functions 'pedAFreq', 'pedGFreq' and
	   'checkMarkers'. If 'missingOutput=TRUE', then information
	   about missing alleles will output, otherwise missing allele
	   information will not be output.

	   introduced a pedigree object containing four elements
	   'ped', 'columns', 'markerNames', and 'Position'.

	   added functions 'readPed', 'readLink', and 'readHapMap' to
	   read pedigree file, data file with PLINK format, and snp
	   files output by HapMap webbrowser to a pedigree object

	   added the functions 'checkMarkers.default' and 'getFounders'

	   added sample info files for subjects in four races (CEU,
	   YRI, CHB, and JPT) in HapMap studies.

	   deleted CAMP example files (because GeneticsBase package has
	   these files) moved geneSet2Ped code to GeneticsBase

	   Remove require.SYMBOL arg from nsFilter, add ... to generic
	   require.SYMBOL may make sense for display purposes, but
	   does not make sense as a gene filtering option since lack of
	   symbol has no biological interpretation.
	   ... was added to the nsFilter generic to give more
	   flexibility to specializing methods.


	   introduced pedigree object containg five elements (ped,
	   columns, markerNames, Position, fileName) in the function
	   Moved geneSet2Ped files from fbat to GeneticsBase

	   deleted power.casectl.R which is no longer used

	   Added GSEMatrix argument to getGEO to allow parsing of
	   SeriesMatrix GSE files Changed GPL parsing to be much
	   faster; other entities to follow


	   Import AnnotationDbi The generics for accessing GO objects
	   moved to AnnotationDbi.  The addition of the package to
	   Depends is hopefully temporary, but allows passing of check
	   for now.

	   Add AnnotationDbi to Depends generic functions for
	   manipulating GO objects moved to AnnotationDbi.  Although it
	   should be possible to only import, that doesn't appear to be
	   working. For now, import _and_ Depend.

	   Fix a bug in termGraphs reverseEdgeDirections doesn't handle
	   edge attributes properly yet so we do the reversing as a
	   last step.

	   Fix node labeling in termGraphs and plotGOTermGraph


	   This is an >= R-2.6.0 package now

	   Remove call to addVigs2WinMenu from Biobase This causes a
	   warning because we don't want to depend/suggest
	   Biobase. Although adding the menu item is a good thing, we
	   hope alternatives will be available and common in R 2.6.0

	   Deprecated buildRepDepGraph and pkgInstOrder Both functions
	   have more powerful equivalents available in the pkgDepTools
	   package. Once removed, the Suggest on RBGL may be able to be
	   removed. The import for tools can be as well.

	   subGraph for graphNEL now properly propagates node and edge

	   minor fixes to the graph vignette and a rewrite of the
	   design discussion

	   introduced the start of some multigraph classes


	   idiogram visuals improved - telomere tips and hashed

	   added a "color.cen" option to idiogram - allows you to
	   change the color of the centromere when margin="i"

	   New Package:

		graph support for KO, KEGG Orthology


		Vince Carey


	    - new argument n.pts for normexp.fit. n.pts=2^10 becomes the
	    default for method="normexp" in backgroundCorrect(). This
	    decreases computation time and introduces some robustness.
	    - backgroundCorrect() now accepts a matrix argument.

	    - decideTests(method="hierarchical") now passes the
	    adjust.method down to the second (t-test) level of
	    testing. Previously the second level testing was always
	    "holm". The spelling is also corrected from "heirarchical"
     	    to "hierarchical".


	  Fixed a bug that occurs when in the multiple tree case not
	  all logic trees are grown.


	  Adding code of checking negative values when using log2

	  Major updates:
	  1. All the major functions compatible with both ExpressionSet and
	  LumiBatch class
	  2. presentCount was removed from the featureData. use
	  detectionCall function to estimate presentCount
	  3. lumiR function now allows user to select the input data
	  4. Add lumiB function for background correction
	  5. lumiExpresso function to encapsulate all preprocessing
	  6. Vignette tutorial has major updates.


  	  bug update to heatplot, added arraylabels to ord

	  Added a message at the end of make.cdf.package() telling end
	  user that they have to install the package before they can
	  use it.

	  Added just a bit more to the message for make.cdf.package,
	  pointing users to make.cdf.env if they don't want to install
	  a package.

	  Fixing a bug related to the load of Rat exon arrays.  Fixing a
	  but related to the load of exon data using APT tools Adding
	  the clustering menu also the raw affy menu Adding PCA with
	  in the classification tools

	  Interface to APT tools DABG p-value calculation was
	  implemented.  Interface to APT tools MiDAS method for
	  alternative splicing detection was implemented.
	  filteringMidas function was implemented in order to selected
	  putative alternative splicing using MiDAS p-values.
	  oneChannelGUI was adapted to the modifications made in

	  Adding MiDAS functions

	  Adding brief Hs annotation data derived by Affymetrix
	  data. This annotation file will be available until
	  annotation libraries for exon arrays will be available

	  Exon arrays analysis: Fixing a bug in the function filtering
	  gene/exon expression on the basis of dabg p-value Adding a
	  new set of functions to perform basic files manipulation
	  within oneChannelGUI Exon arrays analysis: Adding hs gene
	  level annotation to limma TopTable.  TopTable annotation is
	  now done using bioconductor annotation libraries for 3'IVT
	  afymetrix arrays

	  Linking Hs core exon annotation to data generated with APT
	  tools as weel as with those generated with Expression

	  Adding RankProd interface Fixing APT MiDAS DABG

	  Adapting the target file to the use of RPadvance

	  Alternative splicing detection by rank product method was
	  implemented (The efficacy of the method is still under
	  evaluation).  RP and RPAdvance functions from the RanKProd
	  package were gaphically interfaced in opneChannelGUI.


	  Changed pa.calls() to support new ExpressionSet object as
	  input.  Changed pa.calls() output object to list of two
	  matrices (was exprSet). pa.calls() can still accept exprSet
	  input object, but will throw warning message.  Removed
	  extraneous test exprSet.  Single test dataset is now an


	  Applied Kevin Wrights diff for faster nipals. Nipals PCA
	  really should be re-written in C for further speed


	  Update DB_PATH in .onLoad for pd.mapping template
	  If the user has different versions installed in multiple
	  package libraries, we need to get the right one at
	  runtime. Note that for the lazyloading mechanism to work and
	  so that we can create a valid map object, we also need the
	  path in package scope for the initial install.

	  Add templated unit test suite for pdInfo packages
	  Thanks to a patch from Vince, packages generated by
	  pdInfoBuilder now include a minimal RUnit unit test suite.


	  Added R_qnorm_robust_weights to the roaster of C callables
	  so that affyPLM can actually use it (without this, affyPLM
	  does not compile on Windows).

	  Added med_abs to the roaster of C callables (same as for
	  R_qnorm_robust_weights in previous commit.


	  enabled addition of probes' GC content to probeAnno


	  remove slots interactionType, expPubMed and expIntAct from
	  class interactionEntry, and add them to
	  intactInteraction. This changes allow uses map interactions
	  with experiment and interaction detaction methods when one
	  interactionEntry contains multiple experiments. Also
	  modified function psi25complex to provide protein complex
	  IntAct ID in the outputs.


	  Refactor to minimize the WIN32 specific code

	  Use RAWSXP instead of CHARSXP to handle uuid data This patch
	  makes Ruuid compatible with recent changes in R 2.6.0


	  Improved version of denspr (which is used in ebam for
	  categorical variables).

	  Fixed a few bugs.  Now lev in cat.ebam and cat.stat can
	  also handle lists.

	  Now RefSNP IDs can be added to the html output.


	  Added functions (e.g., importGeneSets) to let users import
	  gene sets stored in GMT, GMX, GRP, and XML file formats.


	  fixed a bug in show method for "vsn", and clarified a man

	  Now the parameters for optim (factr, pgtol) are no longer
	  hardcoded, but are passed down from R and are taken from the
	  vsnInput object

	  Better comment on prototype vsnInput In preceding revision,
	  I mistakenly checked in an edited version of vsn.c. I have
	  reverted this back to how it was before.

	  Now the L-BFGS-B parameters are exposed


	  Added wrapper for MassSpecWavelet peak picking on single
	  spectra (findPeaks.MSW) Added some more logic to

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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