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Wed, 30 Apr 2008
affyPLM
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affyPara
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affylmGUI
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affycomp
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affycoretools
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
[/affycoretools] permanent link
affypdnn
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affy
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affyQCReport
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
[/affyQCReport] permanent link
affyio
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affylmGUI
Added LazyLoad: yes to DESCRIPTION file
affylmGUI
Remove some corrections by P. Aboyoun in main.R. The references to exprSet are needed
to check old data files for class name of exprSet and if present retrieve data from them
without needing the exprSet class definition.
also reformat the layout of some code to my liking.
This version ready for release with Bioconductor 2.2
Change references back to exprSet to allow loading of old data files, without using exprSet objects
Reformatting some code
affy
- fixed misplaced parenthesis
- bumped version number
Added na.rm parameter
Added details to the man page
affycoretools
Added AnnotationDbi to the Depends field.
[/affycoretools] permanent link
Wed, 02 Apr 2008
affyPLM
(1.15.10) affyPLM now requires preprocessCore (>=1.1.7)
(1.15.9) rma background correction code from preprocessCore is now used
source files rma_background2.c and rma_background2.h have been removed
affy
(1.17.12) bg.correct.rma now calls the appropriate code from preprocessCore.
Removed the c source code files (rma_background2.c, rma_background2.h).
Removed bg.correct.rma2()
(1.17.10) rma() now uses rma background correction routines from preprocessCore, rather than the previously used internal affy hybrid R/c code implementation
affyPLM
(1.15.9) rma background correction code from preprocessCore is now used
source files rma_background2.c and rma_background2.h have been removed
affyPara
Adds affyPara to bioconductor 2.2
affyPLM
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
affyio
(1.7.17) Minor fixes for CLF/PGF parsers
affyio
(1.7.17) Minor fixes for CLF/PGF parsers
affyPLM
(1.15.8) Remove the source file weightedkerneldensity.c which was not being used by any other code in any way. In otherwords, its removal will have no effect for users of the package.
affyio
(1.7.16) Fix bpmap problems on big endian machines (eg ppc, sparc). This is the same problem that affected and was fixed for little endian machines a number of months ago. To the user it manifested itself with the error message "Error: SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'", but in fact caused by incorrect parsing of the bpmap file version number.
affyio
(1.7.16) Fix bpmap problems on big endian machines (eg ppc, sparc). This is the same problem that affected and was fixed for little endian machines a number of months ago. To the user it manifested itself with the error message "Error: SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'", but in fact caused by incorrect parsing of the bpmap file version number.
affyPLM
Use the recently added Rzlib library in R-devel on Windows.
affy
Use the recently added Rzlib library in R-devel on Windows.
affyio
Put back the -lz reference for referencing zlib for non-Windows (as opposed to -lRzlib) builds.
Updated reference to the zlib library to reflect recent changes in R-devel. In particular, -lz has become -lRzlib.
affyio
(1.7.14) Better checking of potential CEL file corruption. Specifically some vales are now checked to see if they are sensible (ie intensity values should not be negative and x,y locations should not be negative or outside the chip dimensions)
affylmGUI
Replaced support for defunct class exprSet with ExpressionSet.
affypdnn
Replaced usage of defunct class exprSet with ExpressionSet.
affy
Replaced usage of newly defunct exprSet and phenoData classes with ExpressionSet and AnnotatedDataFrame respectively.
affy
Apparent keyboard short-cut accident in earlier commit.
Unexplainable FORTRAN error here, preventing me from going
through the complete R CMD check.
Fixed propagation of changes in subsetting.
affycomp
Fixed usage of se.exprs in ExpressionSet class.
affy
Patch for the bug on se.exprs when subsetting an AffyBatch
(reported by Nicolas Delhomme).
The actual fix differs from Nicolas' patch in the sense that
no new method 'intensity.sd' is added (affy should probably
be on maintenance mode until something unified comes up).
affyPLM
Updated CHANGELOG to reflect changes to 1.15.6.
Replaced reference to soon to be defunct class exprSet with ExpressionSet.
affycomp
Replaced usage of soon to be defunct class exprSet with ExpressionSet.
affycoretools
Removed support for soon to be defunct class exprSet.
[/affycoretools] permanent link
Wed, 20 Feb 2008
affyio
(1.7.13) read.celfile() now includes a additional argument allowing the user to specify reading only the intensity values from the specified CEL file (ie exclude STDEV and NPIXEL)
affyio
(1.7.13) read.celfile() now includes a additional argument allowing the user to specify reading only the intensity values from the specified CEL file (ie exclude STDEV and NPIXEL)
affy
Remove code trying to create MIAME and phenoData using tkWidgets
- The underlying code (in Biobase and more extensively in tkWidgets)
is broken and not easily fixed; widgets can still be used to select
files.
Documentation tidy (removing empty sections and corrected usage)
affyio
(1.7.12) Fixes for C level command console format CEL file parsing. In particular the functions generic_get_detailed_header_info() and gzgeneric_get_detailed_header_info() had problems in some situations where various algorithm parameters were not stored as character strings.