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Bioconductor Changlog.
Thu, 02 Jul 2009
flowCore
Fixed issue with the wrong min range when reading in a fcs file , bumped version no
making sure the range parameter is ignored for clipping after the data has been transformed
flowCore
fixed bug in boundaryFilter and added some more detailed documentation
changed the link fin filter-methods from itself to Subset
flowCore
changed the link fin filter-methods from itself to Subset
flowCore
adding functions to write flowFrames and flowSets to FCS files
flowCore
adding support for multiple data sections in an FCS file
flowCore
making sure all parameters in a flowSet are the same
flowCore
same fix for unionFilters
fixing intersectionFilter
flowCore
bumping the version number
fixing summary for subset filters
flowCore
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
flowCore
Removed unneeded geneplotter dependency.
flowCore
Bumped version no
Updated biexponential transform so that it now calculates
the solution of a generic biexponential function
S(x,a,b,c,d,f) = ae^(bx) -ce^(-dx) +f instead of the logicle function
it was calculating earlier.
Updated Logicle transformation: The implementation of the logicle
transform
was found to be different from that described by Parks et al. A new C
function
was implemented for the logicle transformation reflecting the method
described
in the paper. Additionally, the parameter argument f passed to the
logicle
function was missing a multiplying factor a.
fixing the subsetting of views
We want to be able to add numerics or characters to a workflow
adding support for subsetting operations in workFlows
flowCore
adding support for subsetting operations in workFlows
flowCore
FH taking over maintainership
flowCore
A recent modification in methods::setClass() requires that new("A")
must work for A to be extendable.
I modified the "initialize" method for parameterFilter objects in order
to satisfy this new requirement. Now 'new("parameterFilter")' works (and
flowClust package can extend parameterFilter.
Bumped version to 1.9.22
flowCore
A recent modification in methods::setClass() requires that new("A")
must work for A to be extendable.
I modified the "initialize" method for parameterFilter objects in order
to satisfy this new requirement. Now 'new("parameterFilter")' works (and
flowClust package can extend parameterFilter.
Bumped version to 1.9.22
flowCore
findTimeChannel now returns an empty character vector when more then one potential time channel is found.
flowCore
fixing documentation
update for revised version of the manuscript: logicle reference, flowCore vignette...
flowCore
fixed bug when reading flowSets from an annotated data frame specifying FSC files that are spread across several directories
flowCore
making sure the data is copied when generating a workflow
flowCore
bumping version
'readFlowSet' was overly verbose
allowing to use transformList objects in transform calls
flowCore
modify NAMESPACE
flowCore
fixed default for curv1Filters gridsize
doc fixes
flowCore
added class filterList to hold different filters for the individual frames of a flowSet
flowCore
corrected teh addSignifCurv argument to addSignifCurvRegion
fixed Rd parser warnings
flowCore
fix the call to featureSignif function from the feature package as some parameters have been redifined: addSignifCurv=TRUE now replaces addSignifCurvRegion=TRUE, plotFS=FALSE
flowCore
we are a bit more relaxed about this 10 bit bug in BC FCS files now. When we see the CPX keyword we warn that we fixed the file, if it's not there we still proceed (with 16 bit) but give a more urgent warning
flowCore
add elements in the papaer, especially in the Results and Discussion section
flowCore
removed quotes from do.call
flowCore
more changes
more changes
more changes
flowCore
Added registration for C functions
changed default on how to treat very small numbers
last check for the bmc version of the paper
flowCore
some changes of the paper and addition of work flows
flowCore
As far as I can tell the argument "inv" to compensate is never used or tested in flowCore or plateCore.
Since it is never used, but if you change the value it will give incorrect answers, and since it has been a source of confusion, I thought it best to eliminate it.
I removed it from all function calls, and I commented out any functional lines of code that contained it
and replaced if necessary.
As far as I can tell the argument "inv" to compensate is never used or tested in flowCore or plateCore.
Since it is never used, but if you change the value it will give incorrect answers, and since it has been a source of confusion, I thought it best to eliminate it.
I removed it from all function calls, and I commented out any functional lines of code that contained it
and replaced if necessary.
flowCore
adapting file IO to work on artifactual values
flowCore
edits to the vignette
flowCore
compensate was not passing the inv parameter when the second object was either a data.frame or a compensation
object. I added the ... to the second call inside the function.
flowCore
update to close connection on exit
flowCore
update to close connection on exit
added a isFCSfile function
flowCore
work on the new layout
flowCore
fix biexponential function at zero where it should be zero and not NaN as noticed by Wade Rogers, U Penn; Remove normalisation step of the spillover matrix in the compensation function which was an arbitrary process not justified according to Wade and Florian
flowCore
flowCore to BMC bioinfo