Version: 1.9.4 Category: Minor changes Text: Error on "Affy_snp6_cnchp.txt.bz2" demo file, fixed. Version: 1.9.1 Category: Minor changes Text: Vignette formating in order to meet the guidelines of the "Bioconductor LaTeX Style 2.0". Version: 1.3.4 Category: Major changes Text: EMnormalize() has a new 'priorScale' argument (default to 5) to optimize the gaussian mixture analysis and the identification of the major L2Ratio peaks. Version: 1.3.4 Category: NEW FEATURES Text: The rCGH package now supports Affymetrix OncoScan arrays. As for SNP6.0 and CytoScan arrays, CEL files must be processed by the user first, using either ChAS or Affymetrix Power Tools. See ?readAffyOncoScan for more details. Version: 1.1.8 Text: Version: 1.1.8 Category: Major changes Text: The centralization is now estimated on the distribution of segment values, so after the segmentation step. This mean that now users have to run segmentCGH() before EMnormalize(). Version: 1.1.8 Category: NEW FEATURES Text: plotProfile() gains a 'showCopy' argument. When set to 'TRUE', the profile's y-axis will use the estimated copy numbers instead of the Log2Ratios. Version: 1.1.8 Category: NEW FEATURES Text: The read() functions, used as rCGH-Object constructors, take a supplementary 'ploidy' argument. When known, this value can be used in order to estimate gains and losses expressed in copy numbers. Default to 2. Version: 1.1.8 Category: NEW FEATURES Text: Copy number estimation is also reported in all of the tables, inlcuding the main by-probe table accesible through getCNset(). Version: 1.1.7 Category: NEW FEATURES Text: The user can now specify what supplementary genes annotations to export through the byGeneTable() function. Allowed annotations are those supported by the 'select' method from the 'AnnotationDbi' bioconductor. Version: 1.1.6 Category: BUG FIXES Text: Errors occured when mergin short segments, with respect to the minLen argument in segmentCGH(). Version: 1.1.5 Category: Cleaner version from 1.1.4 Text: Version: 1.1.5 Category: Should not give any warning due to functions masked by imported packages Text: Version: 1.1.4 Category: NEW FEATURES Text: Read Illumina HumanOmniExpress: this function has been temporarily removed. Illumina data require to much memory for annotating probes when probe locations are missing in the data. Version: 1.1.3 Category: NEW FEATURES Text: Read Illumina HumanOmniExpress: see readIllumina() help in the rCGH documentation. Version: 1.1.3 Category: NEW FEATURES Text: New rCGH-generic class for custom arrays: see readGeneric() help in the rCGH documentation. Version: 1.1.3 Category: NEW FEATURES Text: Supports arrays designed according to hg18, hg19 (default) and hg38. To be specified by the user in the read functions and in the byGeneTable function. Version: 1.1.3 Category: NEW FEATURES Text: plotProfile now as pCol and GLcol arguments, for points and gained/lost segments, respectively. Version: 1.1.2 Category: BUG FIXES Text: Major bug fixed in the view() function: one function was not properly called. Version: 1.1.1 Category: Not submitted Text: Version: 1.1.0 Category: New bioconductor devel versioning after release cycle Text: Version: 1.1.0 Category: The first and corresponding bioconductor release version is 1.0.0 Text: Version: 0.99.10 Category: BUG FIXES Text: In view() function: segment colors were not properly assigned. Version: 0.99.9 Category: BUG FIXES Text: In view() function: segment colors were not properly assigned. Version: 0.99.8 Category: BUG FIXES Text: Error when merging probes with duplicated locations on Agilent CytoGenomics 3.0: fixed. Version: 0.99.7 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: byGeneTable() is not a S4 method anymore but S3: as argument, it takes a segmentation table exported from a rCGH object, and not the object itself. As a consequence, byGeneTable() can be used on any segmentation table of the same form as those exported from a rCGH object. Version: 0.99.7 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The full by-gene table is not stored in rCGH object, but built then exported on the fly, using byGeneTable(). Version: 0.99.7 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Supplementary argument in getSegTable(): minLen allows the user to specify the minimal segment length, in Kb. Segments shorter than this value are merged before the segmentation table is exported. The original table is still stored in the rCGH object. Version: 0.99.7 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: New features in plotProfile() and multiplot(): one or multiple genes can be tagged. As for getSegTable(), the minimal segment length (in Kb) can be specified. Version: 0.99.7 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Server version for the interactive viewer is described in the vignette. Version: 0.99.7 Category: BUG FIXES Text: byGeneTable: . In the exported by-gene table, the corresponding segment lengths were not properly reported. . Errors occured when a gene was covered by 2 segments. Version: 0.99.6 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: New cytoScan example file Version: 0.99.6 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Updated vignette Version: 0.99.6 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The rCGH version used is stored in rCGH objects for traceability Version: 0.99.6 Category: NON-VISIBLE CHANGES Text: Supplementary unittests Version: 0.99.5 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: R-3.2.1 is the minimal required version Version: 0.99.4 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: No changes Version: 0.99.4 Category: NEW FEATURES Text: New Version: 0.99.4 Category: BUG FIXES Text: No changes classified as 'bug fixes' under active development)