summaryStats {plateCore} | R Documentation |
This function computes the median fluorescence intensity (MFI) and the
MFI ratio (ratio of test well MFI to negative control MFI) for each
well/channel in a flowPlate
. The predicted percent
positive (Predict.PP) and gate score (Gate.Score) come from a robust
logistic regression of the MFI ratio to either the percentage of positive cells
or the actual count of positive cells.
Predict.PP is the estimated percent positive based on the MFI ratio and
Gate.Score is the number of standardized residuals the sample data point
is away from the best fit line. The glmrob function from the robustbase
package is used for the regression. Results from summaryStats are stored in the
wellAnnotation data.fame
.
summaryStats(data, Events="Percentage", ...)
data |
A |
Events |
The robust logistic regression can be performed using either the percentage of events above the negative control gate ("Percentage") or the actual number of events above the gate ("Actual"). |
... |
optional arguments |
Returns a flowPlate
Errol Strain
library(plateCore) data(plateCore) ## Get the lymphocytes rectGate <- rectangleGate("FSC-H"=c(300,700),"SSC-H"=c(50,400)) pbmcPlate <- Subset(pbmcPlate, rectGate) # Create a flowPlate from the sample data in plateCore fp <- flowPlate(pbmcPlate,wellAnnotation,plateName="P1") # Create a set of negative control gates and then apply them fp <- setControlGates(fp,gateType="Negative.Control") fp <- applyControlGates(fp,gateType="Negative.Control") # Compute summary statistics fp <- summaryStats(fp) # There should now be MFI and MFI.ratio columns in the wellAnnotation head(wellAnnotation(fp))