Merge branch 'collab'

* collab:
  remove as.list from namespace imports
  Fix bug in "[" method for gSetList object that prevents assayData elements from being coerced to class numeric instead of class matrix
  Fix bug when chromosome arm has fewer than 1000 markers
  slight update to droplevels in hmmBeadStudioSet for chromosome arms with few markers
  Fix bug in hmmBeadStudioSet that occurs when a chromosome arm has fewer than 1000 markers
  fix bug in estimation of BAF standard deviation (nonpolymorphic markers were already removed)
  Fix subset method "[" for gSetList class
  Estimate starting values for BAF standard deviations.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@70189 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'collab'

* collab:
  Fixed bug where log R ratios/copy number were not re-centered.
  remove vignettes/VanillaICE.pdf and vignettes/crlmmDownstream.pdf

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@70357 bc3139a8-67e5-0310-9ffc-ced21a209358
@<- has been moved from methods to base, so it no longer needs to
be imported in package NAMESPACEs.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@72298 bc3139a8-67e5-0310-9ffc-ced21a209358
merge with collab

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@72705 bc3139a8-67e5-0310-9ffc-ced21a209358