Question: working with prada objects
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gravatar for Florencio Gonzalez
12.7 years ago by
Florencio Gonzalez30 wrote:
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ADD COMMENTlink modified 12.6 years ago • written 12.7 years ago by Florencio Gonzalez30
Answer: working with prada objects
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gravatar for Nolwenn LeMeur
12.7 years ago by
Nolwenn LeMeur140 wrote:
Florencio Gonzalez <florencio.gblazquez at="" ...=""> writes: > > Hello, I?m new to bioconductor. I need to work with events from cytometer > data. I have to get the region of interest form drawGate and then work with > the events that are into the region selected. How can I access this events? > because drawGate create a gateSet object that only have the boundaries of > the region. > Thanks in advance for the help and sorry for my english > > Florencio Gonzalez Blazquez > Instituto Espa?ol de Oceanograf?a > Centro Costero de Gij?n > avenida Principe de Asturias 70 bis > Espa?a > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Hi Florencio, You need to use the applyGate function on your cytoFrame object: gated.data <- applyGate(myData, myGateSet) This should return an another cytoFrame object. See ?applyGate for more details. If you are just starting with flow cytometry data, I suggest you to have a look at the new flowCore package, available in bioconductor-devel (http://bioconductor.org/packages/2.0/bioc/html/flowCore.html) and soon in the new release of Bioconductor. We hope that the flowCore package will become the 'base' package for many other flow cytometry based packages (e.g. already in development flowViz, flowQ ...). Nolwenn ************************************** Nolwenn Le Meur, PhD Fred Hutchinson Cancer Research Center Computational Biology Program 1100 Fairview Ave. N., M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 Phone: 206.667.5434 Fax: 206.667.1319
ADD COMMENTlink written 12.7 years ago by Nolwenn LeMeur140
Answer: working with prada objects
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gravatar for Florencio Gonzalez
12.6 years ago by
Florencio Gonzalez30 wrote:
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ADD COMMENTlink written 12.6 years ago by Florencio Gonzalez30
Answer: working with prada objects
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gravatar for Nolwenn LeMeur
12.6 years ago by
Nolwenn LeMeur140 wrote:
Florencio Gonzalez <florencio.gblazquez at="" ...=""> writes: > > Thank you for the information. I'll give a try the new package. Just a > question about drawGate. > How can i get two or more populations from a file with the same drawgate > command? I see an option when creating the gate for combine the gating with > another but i get an error > > > pico <- read.fcs("0103") > > pico.sub <- pico[, c(2,4,5)] > > f1 <- drawGate(pico.sub) > Select first variable for gating...FL2-H > Select second variable for gating...FL3-H > Type of gate? (P)olygon or (R)ectangular?p > Draw gate (left click: set point, right click: end drawing). > Determining events within gate...found 1987 > (R)edo this gating, (C)ombine this gating with another one , (P)roceed or > (F)inish? c > Select first variable for gating...FL2-H > Select second variable for gating...FL3-H > Type of gate? (P)olygon or (R)ectangular?p > Draw gate (left click: set point, right click: end drawing). > Determining events within gate...Erro en validObject(.Object) : invalid > class "gate" object: invalid object for slot "boundaries" in class "gate": > got class "list", should be or extend class "matrix" > Hi Florencio, Could you tell me the version of your prada package (sessionInfo)? Using prada 1.10.1, I tried with one of my file and I got the same error message when using combine. However it seems to worked when I am using Proceed instead of Combine. Have you tried? Maybe you should directly contact Florian Hahne the author and maintainer of the package. Cheers, Nolwenn
ADD COMMENTlink written 12.6 years ago by Nolwenn LeMeur140
Answer: working with prada objects
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gravatar for Florencio Gonzalez
12.6 years ago by
Florencio Gonzalez30 wrote:
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ADD COMMENTlink written 12.6 years ago by Florencio Gonzalez30
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