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Bioconductor Changlog.
Wed, 17 Sep 2008
GEOquery
2.5.5
=====
* Added ability to parse single GSEMatrix files from local disk to ExpressionSets.
GEOquery
2.5.4
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* 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
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* 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
Removed usage (or reference) to pstricks tex style in BioC vignettes.
GEOquery
2.5.3
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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
2.5.3
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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
GSEMatrix parsing should be working on windows, so changed vignette
GEOquery
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
GEOquery
fixed for check
GEOquery
Fixed getDirListing to close a temporary textConnection
GEOquery
Rebuilt Vignette
GEOquery
Fixed some problems with vignette and added comments about raw data download
GEOquery
fixed parseGSE when GSEMatrix=FALSE to use textConnections again; was failing to adjust for _table_end stuff
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
Changed references from exprSet to ExpressionSet in the documentation to reflected changes that were made in the code.
GEOquery
Removed the constantly-out-of-date count of samples in GEO from the vignette
GEOquery
2.3.3
=====
* GSM and GDS parsing speedup of 20 to 50 FOLD
GEOquery
* updated vignette to be more GSEMatrix centric for GSE data
* changed a single old "exprSet" instance to "ExpressionSet"
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
2.3.1
=====
* Tried adding back GSEMatrix parsing under Windows. Will see if it builds.
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.