Hi, I am using R2.9.0 and the 2.4 version of Bioconductor. When I try to run a tmixfilter subsetted on a rectangular gate the result is of class logicalFilterResult thus I am unable to access the individual clusters: ################################################# library(flowCore) library(flowClust) data(rituximab) r_filter <- rectangleGate("FSC.H"=c(100,500),"SSC.H"=c(100,500)) # gate boundaries are not meant to be meaningful. t_filter <- tmixFilter("tmix", c("FSC.H", "SSC.H"), K=3) result <- filter(rituximab,t_filter %subset% r_filter) class(result) ################################################ Is that a bug, missing feature or am I missing something? I'd like to be able to see the result of the tmixFilter in the context of the ancestor populations, thus the %subset%. I'am working around that by adding an index vector to the original flowFrame, to be able to do manual subsetting, but it would be nice to to that without this hack. Thanks a lot, Bastian Angermann --

Hi Bastian, this is indeed a feature which wasn't implemented yet. I fixed the code and everything seems to be working as intended now, but I want to give it some more rigorous testing before submitting. I am planning to push that back into the release branch since it is more of a bug fix than feature addition. If you want to be more independent of the types of comparisons between gating steps, you might want to take a look at the workFlow stuff (as described in the package vignette). There you can compute summary statistics for a particular gating operation based on another reference view in the workFlow (via the additional 'reference' argument of the summary method) bw, Florian On 24.04.2009, at 10:30, Bastian Angermann wrote: > Hi, > > I am using R2.9.0 and the 2.4 version of Bioconductor. When I try to > run > a tmixfilter subsetted on a rectangular gate the result is of class > logicalFilterResult thus I am unable to access the individual > clusters: > ################################################# > library(flowCore) > library(flowClust) > data(rituximab) > > r_filter <- rectangleGate("FSC.H"=c(100,500),"SSC.H"=c(100,500)) > # gate boundaries are not meant to be meaningful. > t_filter <- tmixFilter("tmix", c("FSC.H", "SSC.H"), K=3) > result <- filter(rituximab,t_filter %subset% r_filter) > > class(result) > ################################################ > > Is that a bug, missing feature or am I missing something? > I'd like to be able to see the result of the > tmixFilter in the context of the ancestor populations, > thus the %subset%. I'am working around that by adding an index vector > to the original flowFrame, to be able to do manual subsetting, but > it would be nice to to that without this hack. > > Thanks a lot, > Bastian Angermann > -- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor