Hi Jab,
Thanks you for using rflowcyt.
I have created the plotdensity.FCS function to perform some
data quality assessment on 'raw' data but I believe you can use it on
gated data. Depending on your gating approach, I think you can still
read all your
files at once with the read.series.FCS function, which only build a
list
of FCS.object.
Below are 2 dummy examples that, I think, do what you want:
library(rflowcyt)
if (require(rfcdmin)) {
##Obtain the location of the fcs files
pathFiles<-system.file("bccrc", package="rfcdmin")
drugFiles<-dir(pathFiles)
## Read a serie of FCS files
drugData<-read.series.FCS(drugFiles,path=pathFiles,MY.DEBUG=FALSE)
}
##---- First method ------
##Gate your first sample
gate1.range.x <- c(200, 600)
gate1.range.y <- c(200, 600)
gateSample1 <- createGate(drugData[[1]], varpos = c(1, 2), gatingrange
=
c(gate1.range.x,
gate1.range.y), type = "bidcut", comment = "first gate")
##Gate your second
gate2.range.x <- c(300, 600)
gate2.range.y <- c(300, 600)
gateSample2 <- createGate(drugData[[2]], varpos = c(1, 2), gatingrange
=
c(gate2.range.x,
gate2.range.y), type = "bidcut", comment = "first gate")
##Extract data
gateS1 <- extractGatedData(gateSample1,gateNum=1,IndexValue.In=1)
gateS2 <- extractGatedData(gateSample2,gateNum=1,IndexValue.In=1)
##Combine in a list
foo <- list(gateS1,gateS2)
##Draw a density plot for the Foward SCatter parameter for the
##differents aliquots (of the same cell line) tested with different
##compounds.
plotdensity.FCS(foo,varpos=c(1),main="Gated FSC
values",ylim=c(0,0.01),ylab="Density of cells")
##----------Second Method---------
##If the definition of your gate is the same for every sample
gate.range.x <- c(200, 600)
gate.range.y <- c(200, 600)
gatedDrugData <- lapply(drugData,function(x) createGate(x, varpos =
c(1,
2), gatingrange = c(gate.range.x,
gate.range.y), type = "bidcut", comment = "first gate"))
gatedData <- lapply(gatedDrugData,function(x)
extractGatedData(x,gateNum=1,IndexValue.In=1))
plotdensity.FCS(gatedData,varpos=c(1),main="Gated FSC
values",ylim=c(0,0.01),ylab="Density of cells")
Hope it helps,
Nolwenn
**************************************
Nolwenn Le Meur, PhD
Fred Hutchinson Cancer Research Center
Computational Biology
1100 Fairview Ave. N., M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
On Tue, 22 Aug 2006, Jabez Wilson wrote:
> Hi, I've been going through examples in the excellent "rflowcyt"
package, and have a question about the read.series.FCS function.
> The RFlowCyt users guide gives a nice example of reading in 8 FCS
files into a data series using read.series.FCS, and then printing them
out on the same graph e.g.
>
> plotdensity.FCS(drug.fluors, varpos = c(1), main = "FSC for
aliquots \ntreated with different compounds", ylim = c(0, 0.005), ylab
= "Density of cells").
>
> What I would like to do would be to read in these files
separately, perform gating and extract the gated data, and then
combine the subsequent gated FCS objects into a data series and plot
them on the same graph. Is there an easy way to do this? Is it
something to do with the myFCSobj.name="" argument in read.FCS
function.
> Any help/guidance appreciated
> Jab
>
>
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