Question: FlowStats: Normalised flowset is recognised as null after gaussNorm normalisation process
0
gravatar for Wilson Yeo
3.5 years ago by
Wilson Yeo0
Singapore
Wilson Yeo0 wrote:

Hi,

My flowset is recognized as "null" after the normalization process. Attached below are my codes.

Pls kindly help as I am really not sure what really happened and if required I can send the FCS files as well.

Thanks in advance.

Regards,

Wilson

 

library(flowCore)
library(flowViz)

library(flowStats)
library(flowClust)
library(parallel)

LChattodata <- list.files("F://26042016/Limited/Control")
LChadata <- read.flowSet(LChattodata)
LChadata
LChadatatrans <- transform("SSC-Log_Height" = log10, "FSC-Log_Height" = log10, "FL1-Log_Height" = log10, "FL2-Log_Height" = log10, "FL3-Log_Height" = log10, "FL4-Log_Height" = log10, "FL5-Log_Height" = log10, "FL6-Log_Height" = log10, "FL7-Log_Height" =log10, "FL8-Log_Height" = log10, "FL9-Log_Height" = log10, "FL10-Log_Height" = log10, "FL11-Log_Height" =log10) %on% LChadata

##Normalisation of the plot##

RectGate <- rectangleGate(filterId="Counts", "FSC-Log_Height"=c(0,5), "SSC-Log_Height"=c(1.3, 5)) #set coordinates first

RectGatedata <- Subset(LChadatatrans, RectGate)

NRectGatedata <- gaussNorm(RectGatedata, "FL1-Log_Height")$LChadatatrans

ADD COMMENTlink modified 3.5 years ago by Jiang, Mike1.2k • written 3.5 years ago by Wilson Yeo0
Answer: FlowStats: Normalised flowset is recognised as null after gaussNorm normalisatio
0
gravatar for Jiang, Mike
3.5 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:

'gaussNorm' should return a list with items of 'flowSet' and 'confidence', the item ('LChadatatrans') you were referring to simply doesn't exist. Please read the doc and example code in `?gaussNorm`

ADD COMMENTlink written 3.5 years ago by Jiang, Mike1.2k
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