| getMeasureRepAgreement {cellHTS2} | R Documentation |
Calculate the agreement between plate replicates using raw data or normalized data stored in a
cellHTS object.
This function calculates the repeatability standard deviation between replicate plates and the correlation coefficient between replicates. If there are more than 2 replicates, the minimum and maximum correlation between replicates is given. These measures are calculated only for sample wells.
getMeasureRepAgreement(x, corr.method = "spearman")
x |
a configured cellHTS object. See details. |
corr.method |
a character string indicating which correlation coefficient should be computed. Can be either "pearson", "kendall" or "spearman" (default). The correlation is calculated by calling the function
cor. |
Given an already configured cellHTS object (state(x)[["configured"]]=TRUE), this function calculates the repeatability standard deviation between replicate plates and the correlation coefficient between plate replicates using only the sample wells. If there are more than 2 replicates, the minimum and maximum correlation value between pairs of replicates are given.
These measures are calculated using the data values stored in slot assayData of the x.
For a given plate p, the repeatability standard deviation is determined as the square root of the average of the squared standard deviations (sr) calculated for each sample well k by considering the measurement of all of the replicates:
RepStDev_{p} = sqrt{frac{sum{sr^2}}{n_{k} } }
where n_{k} is the total number of sample probes for plate p.
The function generates a list with elements:
"repStDev": matrix with the calculated repeatability standard deviation between plate replicates. It has dimensions nrPlates x nrChannels;
"corrCoef" (if the number of replicates equals 2): matrix with the correlation coefficients between plate replicates. It has dimensions: nrPlates x nrChannels;
"corrCoef.min" (if the number of replicates is greater than 2): matrix with the minimum value of the correlation coefficients between plate replicates. It has dimensions nrPlates x nrChannels;
"corrCoef.max" (if the number of replicates is greater than 2): matrix with the maximum value of the correlation coefficients between plate replicates. It has dimensions nrPlates x nrChannels.
Ligia Bras ligia@ebi.ac.uk
Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.
data(KcViabSmall)
repAgree <- getMeasureRepAgreement(KcViabSmall)
x <- normalizePlates(KcViabSmall, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none")
repAgree <- getMeasureRepAgreement(x)