getMeasureRepAgreement: Measures of agreement between plate replicates from a cellHTS...
In cellHTS2: Analysis of cell-based screens - revised version of cellHTS

Description Usage Arguments Details Value Author(s) References See Also Examples

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.

1	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} = √{\frac{∑{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.

configure, writeReport

    data(KcViabSmall)
    repAgree <- getMeasureRepAgreement(KcViabSmall)
    x <- normalizePlates(KcViabSmall, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none")
    repAgree <- getMeasureRepAgreement(x)