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.factor(Well.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.factor(Well.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.factor(Well.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.factor(Well.Id),transform("FL1-H"=log10)
%on% emkFPcg2[1:12], displayFilter=TRUE,smooth=FALSE,
col=c("red","blue"), filter="Negative.Control")

 


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