fixed minor bugs (added drop=TRUE to the matrix operations) in methylumIDAT.R and related functions.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@71194 bc3139a8-67e5-0310-9ffc-ced21a209358
fix combine(), work with SummarizedExperiment "exports"--Tim Triche patch!

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@71339 bc3139a8-67e5-0310-9ffc-ced21a209358
Added coercions.R--Tim Triche patch!

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@71344 bc3139a8-67e5-0310-9ffc-ced21a209358
Added coercions.R--Tim Triche patch!

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@71345 bc3139a8-67e5-0310-9ffc-ced21a209358
Minor bug fix of estimateM method of MethyLumiM class to hand NA values

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@71587 bc3139a8-67e5-0310-9ffc-ced21a209358
Added ttriche patch to do full conversion between minfi and methylumi and clean up combine

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@71603 bc3139a8-67e5-0310-9ffc-ced21a209358
Fixed a minor bug (missing ")") in MethyLumiSet

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@71618 bc3139a8-67e5-0310-9ffc-ced21a209358
Merged another patch from Tim Triche

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@72866 bc3139a8-67e5-0310-9ffc-ced21a209358
Some updates to get ready for release

* Added patch for coersions.R from ttriche
* cleaned up coersions.R to remove executable "if" statements
* Modified DESCRIPTION and NAMESPACE to deal with coersions updates
* added doc for five missing, undocumented methods



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@74456 bc3139a8-67e5-0310-9ffc-ced21a209358
Removed FDb... from suggests and modified coersions to be more careful with require()

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@74499 bc3139a8-67e5-0310-9ffc-ced21a209358
Removed ALL references to FDb.InfiniumMethylation.hg18 since package is gone

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@74512 bc3139a8-67e5-0310-9ffc-ced21a209358
Addec FDb.InfiniumMethylation.hg19 back to suggests



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@74596 bc3139a8-67e5-0310-9ffc-ced21a209358
bump y of x.y.z version number for BioC 2.12 release

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@75263 bc3139a8-67e5-0310-9ffc-ced21a209358
Bump y in version x.y.z to odd number in devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@75270 bc3139a8-67e5-0310-9ffc-ced21a209358
removed stray require()

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@75390 bc3139a8-67e5-0310-9ffc-ced21a209358
Bugfix in pval.detect(), and in RGChannelSet coercion


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@77864 bc3139a8-67e5-0310-9ffc-ced21a209358
Patches to coercions to/from minfi objects


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@78070 bc3139a8-67e5-0310-9ffc-ced21a209358
Removed BSgenome from imports

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@78139 bc3139a8-67e5-0310-9ffc-ced21a209358
add dependency on matrixStats


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi@81246 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'local-hedgehog'