On 6/18/07, Byron Ellis <byron.ellis at="" gmail.com=""> wrote: > On 6/18/07, M. Jankowski <mjankowski at="" gmail.com=""> wrote: > > Hi all, > > > > > > As you can see, I have some pretty far outliers in all the data sets. > > What procedure would I follow to gate the data to less than 800 for > > "FSC.H" and "SSC.H"? Further, how would I plot the result of the gated > > data? In the context of the HowTo I would call my question "2.1.4: > > Gating and Plotting a flowFrame" > > Section 4 of the How To is entirely about filtering/gating with 4.3 > being the section relevant to your question. In your case you probably > want a rectangleGate of some sort. For example, > > Subset(x,rectangleGate("FSC.H"=c(0,800),"SSC.H"=c(0,800))) > > would cut your frame down to size. As for plotting, this is somewhat > more difficult. The flowViz package has some facilities for plotting a > gate onto a plot of the data, but you'd have to ask Deepayan about > that---I've never actually used it. Yes, flowViz does have some utilities for gates, but they didn't make it to BioC 2.0. You can get the development version from http://bioconductor.org/packages/2.1/bioc/html/flowViz.html (which also has a vignette), and it should work with 2.0 if you are lucky. It may not work with the current devel version of flowCore though. -Deepayan

Byron, This got me back on track! Thank you! Matt On 6/18/07, Byron Ellis <byron.ellis at="" gmail.com=""> wrote: > On 6/18/07, M. Jankowski <mjankowski at="" gmail.com=""> wrote: > > Hi all, > > > > > > As you can see, I have some pretty far outliers in all the data sets. > > What procedure would I follow to gate the data to less than 800 for > > "FSC.H" and "SSC.H"? Further, how would I plot the result of the gated > > data? In the context of the HowTo I would call my question "2.1.4: > > Gating and Plotting a flowFrame" > > Section 4 of the How To is entirely about filtering/gating with 4.3 > being the section relevant to your question. In your case you probably > want a rectangleGate of some sort. For example, > > Subset(x,rectangleGate("FSC.H"=c(0,800),"SSC.H"=c(0,800))) > > would cut your frame down to size. As for plotting, this is somewhat > more difficult. The flowViz package has some facilities for plotting a > gate onto a plot of the data, but you'd have to ask Deepayan about > that---I've never actually used it. > > > > > The flowSet discussion in the HowTo does cover filtering and gating. > > When I attempt to read my file in as a flowset I get errors. > > > > Section 2.2.1 give the instruction: > > > frames <- lapply(dir(system.file("extdata", "compdata", "data", > > + package = "flowCore"), full.names = TRUE), read.FCS) > > > as(frames, "flowSet") > > When reading from files it is almost always best to use read.flowSet, > which automates much of this process. > > > > > I'm not certain how to put my "/home/mdj/Rdata/" directory into the > > context of the system.file function. Here is my best attempt: > > > frames <= lapply("/home/mdj/data/Rdata/", readFCS) > > Your example differs from the example in the How To in two ways. > First, the lapply() is actually performed on the directory listing. > For example, > > lapply(dir("/home/mdj/data/Rdata",patt="\\.fcs$"),readFCS) > > is more likely to do what you want. The inclusion of a pattern ensures > that only things with the "fcs" extension will be used. However, it > mostly serves as an example by way of construction so you shouldn't > need to use it unless you need to do something that read.flowSet > cannot (like grab the FCS files from URLS or something). > > Also, you have <= instead of <-. <= is an inequality. Personally, I > hate <- with a passion (b[b<-1] = 0. Whoops.) and thus tend to use > just =, unless it is impossible for some reason (very rarely). > > > Error: object "frames" not found > > > > When I attempt "read.flowSet": > > > > > read.flowSet("/home/mdj/Rdata/") > > This is because the first parameter of read.flowSet is actually a > pattern not a path (I know, the opposite of dir... but this is the way > things go). This is because you're usually in the same directory as > your FCS files. You actually want: > > read.flowSet(path="/home/mdj/Rdata/") > > or something similar. > > > These errors have me stumped. I think the organization of this library > > is quite keen. I like the flowFrame object in what I think of as a > > flowSet vector (with nice header). Would someone show me how to: > > > > 1) gate my data for the 'flowFrame' object and then plot the gated data? > > > 2) work my way through creating a flowSet object? I think my main > > problem is that I am clumsy with the system.file syntax. > > > > My apologies if these questions are answered elsewhere. If this is the > > case please point me in the right direction. > > > > Any and all help is appreciated. Thanks! > > > > Hope that helps. > > > Matt > > > > _______________________________________________ > > 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 > > > > > -- > Byron Ellis (byron.ellis at gmail.com) > "Oook" -- The Librarian >