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affycoretools
Added AnnotationDbi to Imports

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affycoretools
Removed support for soon to be defunct class exprSet.

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affycoretools
Converted many of the dependencies from Depends to Imports. This removes the functions in these packages from the search path, which will speed things up.

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affycoretools
One more fix to account for changes to biomaRt.

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affycoretools
Bugfixes for changes in bioma
Modified biomaRt-specific functions to account for the fact that the MySQL interface has been removed from that package.
Made change to reflect removal of Dilution from the affy package. The data resides in affydata.

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affycoretools
Fixed two bugs in probes2tableBM

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affycoretools
Removed hgfocus from Suggests, as it isn't used.
more tweaks to modify the suggests/depends to be on .db annotations
changed the vignette depends entries

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affycoretools
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.

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affycoretools
Small fix to hyperGoutput. The output of annotation(GOHyperGResult) no longer contains the .db suffix, so this has to be added back on.

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affycoretools
Updated BiocViews.

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affycoretools
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

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affycoretools
Small bug in vennSelectFC that resulted in incorrectly named fold change columns in the output.

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affycoretools
Added AnnotationDbi to imports section in NAMESPACE file.

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affycoretools
Added imports(AnnotationDbi, get) so things like get(goid, GOTERM) will work.

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affycoretools
Added AnnotationDbi to the Depends field.

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affycoretools
Last of the changes to biomaRt-specific functions, due to the removal of MySQL interface from biomaRt.

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affycoretools
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.

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affycoretools
Removed hgfocus from Suggests, as it isn't used.

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affycoretools
updated an example, as affybatch.example is now gone

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affycoretools
Bumped version number so that previous changes will be pushed out.
Removed dependency on hgfocus.db from affycoretools_biomart vignette.

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affycoretools
Small bugfix to plotPCA() so arguments x.coord and y.coord now actually work.

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affycoretools
Removed a martDisconnect(mart) from a vignette. This was breaking the package because the MySQL interface is now gone.

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affycoretools
Bugfix missed in last commit.

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