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
>
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>
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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
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
