About
Click here
to learn more about this blog.
Packages
Click on a link
for updates to that package only.
Subscribe
Subscribe to the
Bioconductor Changlog.
Tue, 13 Oct 2009
affxparser
Version: 1.15.5 [2009-02-14]
o Fixed a bug related to SET_VECTOR_ELT/SET_ELEMENR used on strings.
Affected readChp.
o Fixed a bug related to naming of the list structures (we assigned
a list instead of a character as the name. Affected readCdfUnits and
readCdfCellIndices.
o Updated Fusion from 1.11 to 1.12.
o Fixed a bug in the example for readCdfUnitsWriteMap: the package
AffymetrixDataTestFiles was misspelled, so the tests were never run.
affxparser
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
affxparser
Robert adding in the necessary files to Makevars for reading CHP files
affxparser
Version: 1.13.4 [2008-08-05]
o Renamed the HISTORY file to NEWS.
o Now help(createCel) (and its example) clarifies that
the template CEL header can be of v3 (ASCII),
v4 (binary;XDA), or v1 (binary;Calvin).
affxparser
CPP code for parsing CHP tiling arrays
code of the parsing chp files
affxparser
Added the feature of reading the DAT header of CEL files
affxparser
Version: 1.15.6 [2009-02-20]
o Added optional argument 'newChipType' to convertCel() for overriding
the default chip type. Useful for updating the formal chip type
of old CEL files.
o Removed all gc() calls in convertCel().
affxparser
Last commit contained an embarrassing bug. Fixed
Fixed the loading of R.utils in findFiles. This loading had bad consequences for R CMD check - unfortunately. A better fix would be to take care of the problem at its root.
affxparser
o (unexposed) function .pgfProbeIndexFromProbesetIndex failed to
handle last probe correctly
affxparser
Add necessary headers to Windows Makefile
affxparser
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affxparser
Bugfix in .initializeCdf thanks to bug report from E. Purdum
affxparser
Fixed up writeTpmap as per bug report on BioC
affxparser
Fixed a bug in readChp reported on Bioc mailing list, also fixed a problem in compareCels from yesterdays update of readCelHeader. This time it passes check.
affxparser
Fixed up writeTpmap as per bug report on BioC
affxparser
Version: 1.11.5 [2008-02-29]
o Updated cdfMergeStrands() to merge any even number of groups,
not only units with two or four group pairs.
o BUG FIX: The code in findFiles() for testing if R.utils is loaded
or not in v1.11.4 was not correct making it fail to detect R.utils.
Version: 1.11.4 [2008-02-20]
o Now findFiles() and hence findCdf() is only utilizing the R.utils
package if it is already loaded. It will no longer try to load R.utils.
o Added argument 'allFiles=TRUE' to findFiles().
o Updated readCcg() according to the newer file format specifications.
Now it is possible to do low-level reading of copy-number CNCHP
files generated by the Affymetrix Genotype Console v2.
affxparser
Added a Makefile, bumped version
Fixed small as.integer() bug in tpmap2bpmap
affxparser
Version: 1.15.4 [2009-02-10]
o readCcg() and readCcgHeader() no longer give warnings
on 'truncating string with embedded nul' in rawToChar().
These warnings made no difference, but were annoying.
Version: 1.15.3 [2009-01-22]
o Fixed a minor Rd problem.
affxparser
Fixed the loading of R.utils in findFiles. This loading had bad consequences for R CMD check - unfortunately. A better fix would be to take care of the problem at its root.
affxparser
Moved readPgf, readClf to *Env, added readPgf,readClf,readClfHeader,readPgfHeader. These now return lists and use an indices argument to specify which probesets should be read. The value of these over the environment function is questionable.
updated to Fusion 1.0.10b
affxparser
Added a check to make sure that the indices are sorted for now. The larger fix requires reading the file in a different way because of the linked list type setup. Or it requires a little bit of fixing up on the way out, which might be the appropriate way.
affxparser
Version: 1.15.2 [2008-12-30]
o Same bug fix as in release version v1.14.2.
Version: 1.14.2 [2008-12-30]
o BUG FIX: readChp() would not read all data. Thanks
Gabor Csardi for reporting this and providing a patch.
affxparser
Fixes include statements in Fusion, trying to fix an issue with GCC 4.3. Fix suggested by Herve Pages
affxparser
fixed a minor doc bug
affxparser
Really updated to Fusion 1.10b. Fixed an error in the help page for readCel.R
affxparser
more mods for CHP files
affxparser
updated to Fusion 1.0.10b
affxparser
more updates for CHP files, MultiData files begun
affxparser
Version: 1.13.5 [2008-08-09]
o BUG FIX: writeCdf() would write 'CustomSeq' units as 'Tag' units,
and vice versa. This means that *ASCII* CDFs containing such
units and converted with convertCdf() would be have an incorrect
unit type for these units. Also, unit type 'Copy Number' is
reported as "copynumber" and no longer as "unknown".
o BUG FIX: The increase of the internal buffer for reading the
'refseq' header field of ASCII CDFs that was done in v1.11.2
was mistakenly undone in v1.13.3.
o Made readCdf() recognize more unit types.
affxparser
more changes to the CHP parsing
affxparser
added code for legacy genotyping arrays
mostly working on the Resequencing arrays
fixed a couple of bugs in the CHP parsing code
more mods for CHP files
affxparser
Version: 1.11.3 [2007-12-01]
o Removed argument 'reorder' from readCel() and readCelUnits()
since its name was misleading (the returned value was identical
regardless of 'reorder', but the reading speed was faster when
'reorder' was TRUE, which is how it is now hardwired).
affxparser
Version; 1.11.6 [2008-03-04]
o Add ability to parse PGF and CLF files
affxparser
Fixed the CDF header bug: line 723 and 724 has the number 65000 changed to 400000
Updated to Fusion SDK 1.11
affxparser
Version: 1.13.7 [2008-08-23]
o SPEED UP: readCcg() is substantially faster after removing
all gc() calls.
Version: 1.13.6 [2008-08-21]
o Updated Fusion SDK from 1.0.10b (Jan 2008) to 1.0.11 (July 2008).
affxparser
Version: 1.17.3 [2009-05-29]
o Added applyCdfGroupFields() and cdfSetDimension().
Version: 1.17.2 [2009-02-20]
o BUG FIX: readChp() would crash (segmentation fault) for (at least)
some CHP files for GenomeWideSNP_5 generated by Affymetrix Power Tools.
o BUG FIX: Updated compareCels() to work with new readCelHeader().
Version: 1.17.1 [2009-05-09]
o Now readCelHeader() also reads DAT headers from Calvin CEL files.
Version: 1.17.0 [2009-04-20]
o Devel version bumped because of the new Bioconductor release.
Version: 1.16.0 [2009-04-20]
o Release version bumped because of the new Bioconductor release.
affxparser
moved the updates from release to devel
affxparser
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.