getMeasureRepAgreement {cellHTS2} | R Documentation

## Measures of agreement between plate replicates from a cellHTS object

### Description

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.

### Usage

    getMeasureRepAgreement(x, corr.method = "spearman")

### Arguments

`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`.

### Details

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.

### Value

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`.

### Author(s)

Ligia Bras ligia@ebi.ac.uk

### References

Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.

### See Also

`configure`, `writeReport`

### Examples

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

[Package cellHTS2 version 2.4.1 Index]