Entering edit mode
Sancho, Jose
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80
@sancho-jose-3937
Last seen 10.2 years ago
Hello all,
I was planning on using plateCore for multiple plates analysis, almost
a
100 plates overall and I am having some difficulties as to how it's
best
to proceed.
So I have a few questions:
1. Using xyplot(`FL1-H` ~ `FSC-H` |
as.factorWell.Id),transform("FL1-H"=log10) %on% emkFPcg2[1:12],
displayFilter=TRUE,smooth=FALSE, col=c("red","blue"),
filter="Negative.Control") I get plots with FL1-H scale from 0 t0 3,
but
all my events are from 2.5 to 3. All the samples have most of the
events
on the first decade.
Why is this happening? I did not have this problem with other
samples....
2. I do not have negative control in each plate, only in one well
in one plate, how can I use this for all of the plates? I am running
batches of 10+ plates, single color, 5K collected. What would the max
number of plates that could be combined?
See history below
Thanks
Jose Sancho
Genzyme FCCF
wellAnnotation<-read.table(file("C:/Documents and
Settings/sanjo05/Desktop/PLATES/table.txt"),header=TRUE,
stringsAsFactors=FALSE)
emkPlate10<-read.flowSet(path="C:/Documents and
Settings/sanjo05/Desktop/PLATES/EMK092110P10",transformation=FALSE)
wellAnnotation<-read.table(file("C:/Documents and
Settings/sanjo05/Desktop/PLATES/table.txt"),header=TRUE,
stringsAsFactors=FALSE)
emkFP10 <- flowPlate (emkPlate10, wellAnnotation,
plateName="EMK092110.001")
pData(phenoData(emkPlate10))[1,]
fs <- plateSet(emkFP10)
xyplot(`SSC-H` ~ `FSC-H` | as.factorWell.Id), emkFP10[1:4],
displayFilter=TRUE, smooth=FALSE, col=c("red", "blue"))
normGate <-norm2Filter("FSC-H", "SSC-H", scale.factor=2)
xyplot(`SSC-H` ~ `FL1-H` | as.factorWell.Id), emkFP10[1:4],
displayFilter=TRUE, smooth=FALSE, col=c("red",
"blue"),filter=normGate)
emkFP10.gated <- Subset(emkFP10,normGate)
emkFPcg10<-
setControlGates(emkFP10.gated,gateType="Negative.Control",numMads=5)
emkFPcg10 <-applyControlGates(emkFPcg10)
wells
<-unique(subset(emkFPcg10@wellAnnotation,Negative.Control=="A01",
select="name")[,1])
xyplot(`FL1-H` ~ `FSC-H` | as.factorWell.Id),transform("FL1-H"=log10)
%on% emkFPcg2[1:12], displayFilter=TRUE,smooth=FALSE,
col=c("red","blue"), filter="Negative.Control")
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