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Bioconductor Changlog.
Tue, 13 Oct 2009
GEOquery
2.5.3
-----
Thanks to Jonathan Dreyfuss for suggesting a change to deal with 'null' in GSEMatrix files
* Added na.strings=c('NA','null','NULL') to the parseGSEMatrix read.delim() call
2.5.2
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* Changed GDS2MA and GDS2eSet to have the default behavior of fetching the Annotation GPL file for inclusion in the eSet or MAList
2.5.1
====
* Added ability to download Annotation GPL files that often include more information than standard GPL files because they are curated by GEO against the Entrez Gene database
GEOquery
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
GEOquery
cleaned up and documented some old code. Also, did away with gunzipping and used gzfile directly.
GEOquery
fixed parseGSE when GSEMatrix=FALSE to use textConnections again; was failing to adjust for _table_end stuff
GEOquery
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
GEOquery
Rebuilt Vignette
GEOquery
Fixed some problems with vignette and added comments about raw data download
GEOquery
2.5.3
-----
Thanks to Jonathan Dreyfuss for suggesting a change to deal with 'null' in GSEMatrix files
* Added na.strings=c('NA','null','NULL') to the parseGSEMatrix read.delim() call
GEOquery
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
fixed getAndParseGSEMatrices to use gzfile--thanks to Martin Morgan for doing the homework and suggesting a fix for using gunzip (which does not work on Windows).
added citation
GEOquery
Changed references from exprSet to ExpressionSet in the documentation to reflected changes that were made in the code.
GEOquery
Added RUnit as a "suggests:" to fix warning
GEOquery
2.3.3
=====
* GSM and GDS parsing speedup of 20 to 50 FOLD
GEOquery
fixed for check
GEOquery
2.3.2
=====
* Hopefully fixed GSEMatrix parsing on Windows. Thanks to Henrik Bengtsson and Uwe Ligges for pointers. The issue was download.file using text mode, which on Windows for .gz files causes problems.
* GSEMatrix parsing is now the default for getGEO when downloading GSE records. This ends up being many orders of magnitude faster for most GSE records.
GEOquery
Removed usage (or reference) to pstricks tex style in BioC vignettes.
GEOquery
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.
GEOquery
Fixed getDirListing to close a temporary textConnection
GEOquery
Removed the constantly-out-of-date count of samples in GEO from the vignette
GEOquery
Fixed (using a bit of a hack) the problem of reading
an entire table, including the !sample_table_end
when the IDs are numeric.
GEOquery
Adding more tests
GEOquery
2.3.1
=====
* Tried adding back GSEMatrix parsing under Windows. Will see if it builds.
GEOquery
GSEMatrix parsing should be working on windows, so changed vignette
GEOquery
added URL
GEOquery
* updated vignette to be more GSEMatrix centric for GSE data
* changed a single old "exprSet" instance to "ExpressionSet"
GEOquery
Adding more tests
Began to add a test suite based on RUnit. The tests are pretty simple right
now and do not catch all known bug fixes. The bug fix tests will need to be
added over time.
Took out a sentence in the vignette about improving GSE data handling
Bumped version number to catch last changes
VERY significantly improved speed of GSE SOFT format parsing (i.e.,
when GSEMatrix=FALSE). This is a speedup of a couple of orders of
magnitude.
Added an example GSE, GDS, GPL, and GSM to extdata for testing purposes.
GEOquery
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
GEOquery
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
GEOquery
2.5.4
-----
* Added na.strings argument ('null','NA','NULL') to the read.delim statements in fastTabRead and parseGSEMatrix to deal with null values more appropriately. Thanks to Jonathan Dreyfuss for the suggestion.
2.5.4
-----
* Added na.strings argument ('null','NA','NULL') to the read.delim statements in fastTabRead and parseGSEMatrix to deal with null values more appropriately. Thanks to Jonathan Dreyfuss for the suggestion.
GEOquery
bump version number--no other changes
In getGEO.R, change con <- null to con <- NULL to fix "no "null" object
found" build error produced by R CMD build.
Inclement the version number for the change made for getGEO.R.
GEOquery
fixed parseGSE when GSEMatrix=FALSE to use textConnections again; was failing to adjust for _table_end stuff
GEOquery
Added support for supplemental file downloads for all GEO datatypes
GEOquery
2.5.5
=====
* Added ability to parse single GSEMatrix files from local disk to ExpressionSets.