CHANGES

### CHANGE log for package oligo ###

12-8-2008: BC

** added binary snr file for 50k,250k arrays (crlmm)

** fixed pmPosition for NGS tiling

12-6-2008: BC

** read.celfiles was modified

** added: checkValidPhenodataForFiles, createPhenodataFromIds, createDefaultMiame, checkChipTypes
these helpers can (and will) be used for read.xysfiles

Changes made by Matt Settles 12-4-2008

** All changes should generally have effect on only Affy Tiling, ST and expression arrays.
modifed read.celfiles to appear more like read.affybatch, should present a noticable change

03-8-2009: BC

** Copied rma2.c from Affy... API for RMA changed.

** Added a basicRMA function in utils.R

** Added an rma method for Exon arrays.

** Changes previous rma method (originally for FeatureSet objs) to handle only ExpressionFeatureSet objects. The method is now in methods-ExpressionFeatureSet.R.

** RMA for Exon: we summarize to the probeset level. The output, an ExpressionSet, contains in its featureData slot annotation for further processing (to the exon/gene-level)

03-9-2009: BC - committed version 1.7.23

** Added support for Gene ST Arrays (structure very similar to Exon)

** Added RMA for Gene ST arrays. The only difference from RMA/Exon is the SQL query that includes an INNER JOIN to account for multiplicity (1:N mapping from probe to probeset). This is implemented in methods-GeneFeatureSet.R

03-17-2009: BC - committed version 1.7.25

** Modified rma method to extract information from pmfeature and bgfeature (bgfeature is assumed to contain PM probes only) tables. The qcpmfeature table will not be available for pdInfoBuilder objects on what I call 'version 2.0'.

03-24-2009: B Carvalho - committed versioin 1.7.29

** Several small changes to clean up package

** Added TilingFeatureSet2, read.xysfiles2, read.celfiles2, getNgsColorInfo as an attempt to appropriately handle two colors applications of tiling arrays.

03-25-2009: B Carvalho

** Changes to accommodate sequence methods

03-26-2009: B Carvalho

** Improved NAMESPACE

** Added basicRMA() to interface with RMA C-code

04-02-2009: B Carvalho

** Added affyio to parse CEL files. This is an initial attempt. 'affyio' provides a much faster parser and also allows users to read in CEL.gz files.

04-06-2009: B Carvalho

** list.celfiles() also returns .cel.gz files

04-07-2009: B Carvalho

** Cleaned up code.

04-13-2009: B Carvalho

** Changed read.table to read.delim in getCrlmmSummaries so filenames with white spaces do not break the code.

04-16-2009: B Carvalho

** Removed some unused code

04-24-2009: B Carvalho

** Added getContainer help page

** Added more verbosity to read.xysfiles

04-29-2009: B Carvalho

** Fixed documentation for read.celfiles and read.xysfiles

** Changed error message (when annotation cannot be loaded)

05-07-2009: B Carvalho

** Added C-code to parse XYS files

05-09-2009: B Carvalho

** Fixed sampleNames that was being ignored

** Removed extra ordering for XYS files

05-11-2009: B Carvalho

** Fixed bug with getMetadata2: if user passes a phenoData object,
this would be incorrectly combined with other objects because the
sampleNames were different.

05-21-2009: B Carvalho

** Fixed bug with basicRMA.

07-31-2009: B Carvalho

** Fixed warnings at the C-level

** More strict versions of dependencies

08-05-2009: B Carvalho

** Replaced require(annotation(obj)) by requireAnnotation(annotation(obj))

08-06-2009: B Carvalho

** RMA, for Exon and Gene arrays, is now possible to the gene-level

08-14-2009: B Carvalho

** Fixed image() for Affymetrix arrays

08-18-2009: B Carvalho

** Fixed and improved behavior of boxplot() for ExpressionSet and FeatureSet objects

08-20-2009: B Carvalho

** Added more details to the documentation associated to list.celfiles() and list.xysfiles()

10-21-2009: B Carvalho

** Fixed some probles in the vignettes

11-09-2009: B Carvalho

** removed rma_background2.c and rma_background2.h; preprocessCore is used instead.

11-12-2009: B Carvalho

** added rma() for quick and informal inspection of CNPs

12-02-2009: B Carvalho - committed version 1.11.6

** brought methods from oligoClasses

12-03-2009: B Carvalho - committed version 1.11.8

** brought documentation from oligoClasses

12-06-2009: B Carvalho - committed version 1.11.10

** removed se.exprs

01-22-2010: B Carvalho - committed version 1.11.11

** added support for large objects (via bigmemory)
    read.celfiles / read.xysfiles / read.celfiles2 / read.xysfiles2
** added support for parallel computing (via snow - requires bigmemory)
** implemented backgroundCorrect for matrix and big.matrix
** implemented normalize for matrix and big.matrix
** implemented summarize for matrix and big.matrix
** implemented rma workflow for big.matrix
** removed doc for list.celfiles, which is now in oligoClasses
** removed useAffyio argument from read.celfiles and read.celfiles2
** now imports 'digest'
** rma (expression) supports large objects and parallel computing
** rma (exon/gene) supports large objects and parallel computing
** added some diagnostic messages when package is attached
   on large dataset and parallel computing support
** added hooks for bigmemory/snow packages

02-02-2010: B Carvalho - committed version 1.11.12

** fixed bug in rma with big objects in which sample indices were
   missing if user chose to skip background correction.

02-11-2010: B Carvalho - v 1.11.14

** exported pmChr
** fixed .onAttach

02-18-2010: B Carvalho - v 1.11.15

** support to large datasets is now given through 'ff'
** digest is no longer a dependency

02-26-2010: B Carvalho - v 1.11.18

** added darkColors and seqColors, which will interpolate along some
   colors I like and generate a vector of length N to be used to set
   colors when plotting
** added plotM method for SnpSuperSet
** added getAffinitySplineCoefficients (estimate affinity spline coefs) 
   and getBaseProfile (estimate actual effect and optionally plot it)
** added Hands-On vignette

03-01-2010: B Carvalho - v 1.11.22

** fixed vignette scheme
** (x.y.20) fixed getFid*

03-04-2010: B Carvalho - v 1.11.23

** fixed format of NEWS
** fixed NAMESPACE/DESCRIPTION: packages now in Imports
** removed getMetadata(2) and other unused functions
** added documentation to getBaseProfile and getAffinitySplineCoefficients.
** removed reference to genDatasetUID (1.11.26)

03-10-2010: B Carvalho - 1.11.29

** moved some docs (cluster related) to oligoClasses

03-11-2010: B Carvalho

** (1.11.30) replaced oLapply by ocLapply(..., neededPkgs="oligo")
** (1.11.31) got rid of sendBO2env

03-22-2010: B Carvalho

** (1.11.32) fixed probeNames for Gene/Exon arrays (Mikhail Pachkov)

03-30-2010: B Carvalho

** (1.11.33) fixed documentation to pass R CMD check

04-06-2010: B Carvalho

** (1.11.34) fixed check for getM on TilingFeatureSet
             fixes for crlmm code (not to be seen by user, code rewrite)

04-16-2010: B Carvalho

** (1.11.36) changed getContainer to extract 'type' from (pm/bg)feature table
** (1.11.38) approp. documented rma for gene/exon arrays

05-05-2010: B Carvalho

** (1.13.1) fixed bugs: image / bg / bgindex / pmChr / bgSequence for Gene and Exon arrays
** (1.13.1) added support to gzipped XYS files
** (1.13.3) fixed bugs with subsetting of Gene chips / docs