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Bioconductor Changlog.
Wed, 21 May 2008
AnnotationDbi
Fixes annotation and map counts bugs in Inparanoid packages.
This patch just repairs minor bugs in the code that generates the
inparanoid packages.
[/AnnotationDbi] permanent link
ShortRead
Hi Martin, I tried to make the language a little bit more precise. First
wanted to send you an email, but this is so trivial that I hope it is OK
with you that I just put it in svn...
CoCiteStats
tried to rework some of this to make better use of the AnnotationDbi
interface
Biostrings
Minor code changes for marginal improvements.
Added the ability to use pairwiseAlignment when the pattern object is an XStringSet argument when scoreOnly = TRUE. This involved a refactoring of the code and a renaming of some arguments.
GenomeGraphs
Some reasonably large changes which will probably mess up R CMD CHECK, but need to get these in here at some point. They include a new object which should replace the various forms of annotation plotting.
[/GenomeGraphs] permanent link
affxparser
Fixed up writeTpmap as per bug report on BioC
rHVDM
force minpack.lm version
force minpack.lm version
oneChannelGUI
Adding a QC for raw data for genechip EXON 1.0 ST:
Using APT tools positive and negative control probes, i.e. exon and introns of known housekeeping genes, are extracted form the CEL files, log2 transformed and plotted to give an idea of the array signals.
[/oneChannelGUI] permanent link
lumi
Update getControlData function to allow inputting "control gene data.txt"
xcms
Fixing typo in profBinLinBase
arrayQualityMetrics
- same colour groups across plots
[/arrayQualityMetrics] permanent link