Dear Chao-Jen, Thanks for the prompt reply. At the moment I am planning to use a simple rectangle gate. What I don't yet understand is how I can specify as the "parent" gateview, the union of two gateviews in the workflow. If at all possible. I've tried to come up with a toy example. I don't pretend it makes any biological sense, but hopefully it will demonstrate what I am trying to achieve. As you will see I am stuck with the implementation of "gateZ" at the end of the script. Any suggestions welcome. Thanks in advance Alessandro ############################## library(flowCore) library(flowViz) library(flowUtils) library(flowStats) data(GvHD) myFCS <- GvHD[[1]] # Get a sample Flow Frame # Create Gates gateA <- rectangleGate(`FSC-H`=c(330,600),`SSC-H`=c(0,200),filterId="GateA") gateB <- rectangleGate(`FSC-H`=c(150,320),`SSC-H`=c(0,200),filterId="GateB") #Initialize workflow and apply transformations # to non(FSC,SSC) parameters wf <- workFlow(myFCS) t.logicle <- transformList(from=colnames(myFCS)[4:7],logicleTransform(),transforma tionId="logicle") add(wf,t.logicle) # Applt gateA and gateB add(wf,gateA,parent="logicle") add(wf,gateB,parent="logicle") # Use lymphGate to the positive selections of gate A and gate B gateC <- lymphGate(Data(wf[['GateA+']]), channels=c("SSC-H", "FSC-H"), eval=FALSE, filterId="GateC") add(wf,gateC$n2gate,parent="GateA+") gateD <- lymphGate(Data(wf[['GateB+']]), channels=c("SSC-H", "FSC-H"), eval=FALSE, filterId="GateD") add(wf,gateD$n2gate,parent="GateB+") # Plot the diagram (very cool feature btw) plot(wf) # Apply GateZ to the UNION of cells in GateD+ and GateC+ gateZ <- rectangleGate(`FL2-H`=c(1.6,5)) ## ## I am stuck HERE :0) ## ?? add(wf,gateZ ,parent=(GateD+ | GateC+)) ?? ## ############################## On Fri, 4 Feb 2011 13:41:07 -0800 (PST), "Wong, Chao-Jen" <cwon2 at="" fhcrc.org=""> wrote: > Hi, Alessandro, > > What kind of filter you are going to apply to wf[["Lymphocytes+"]] or > wf[["Monocytes-"]]? There are four types of actions you can apply to > a work flow object. They are compensation, transformation (logicle, > asinh, and etc.), normalization, and gating/filtering (rectangleGate, > rangeGate, norm2Filter, kmeansFilter and etc.) actions. As long as > your filtering actions are in these categories, and then of course > you > can apply them to any of the gate views (by specifying the "parent" > argument). There are some extra gating/filtering actions implemented > in the flowStats packages that you might find useful. > > > Chao-Jen > > ----- Original Message ----- > From: "Alessandro Di Cara" <rmailing at="" di-cara.com=""> > To: bioconductor at r-project.org > Sent: Thursday, February 3, 2011 2:38:13 PM > Subject: [BioC] flowCore workflows and logical operations on gate > views > > Dear List, > > I am using the flowCore and flowViz packages to perform some flow > cytometry analyses on clinical data. > I find the packages extremely useful. > > Some of the gating strategies I have to implement are quite tricky > and I > would like to use the "Work Flows" system > described in the flowCore reference manual. So far, I find this > approach > very efficient, not only for accessing the intermediate analysis > steps > of my analysis but also for solving memory issues when loading many > FCS > files. > > I am stuck with the implementation of logical operations on the gate > views of a workflow > > For example let's say I have a workflow object "wf" with two gate > views > > wf[["Lymphocytes+"]] > wf[["Monocytes-"]] > > I would like to apply a filter on cells that are in the > wf[["Lymphocytes+"]] OR wf[["Monocytes-"]] gate views. > > Can this be done using the work flows system? Would these operations > be > reflected in the work flow graph plot ? > > Thank you in advance for you help > > All the best, > > Alessandro Di Cara > / > > / > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor