bapred (version 1.1)

skewdiv: Skewness divergence score

Description

This metric presented in Shabalin et al. (2008) is concerned with the dissimilarity across batches of the skewnesses of the observation-wise empirical distributions of the data.

Usage

skewdiv(xba, batch)

Arguments

xba

matrix. The covariate matrix, raw or after batch effect adjustment. observations in rows, variables in columns.

batch

factor. Batch variable. Each factor level (or 'category') corresponds to one of the batches. For example, if there are four batches, this variable would have four factor levels and observations with the same factor level would belong to the same batch.

Value

Value of the metric

Details

For two batches j and j* (see next paragraph for the case with more batches): 1) for each observation calculate the difference between the mean and the median of the data as a measure for the skewness of the distribution of the variable values; 2) determine the area between the two batch-wise empirical cumulative density functions of the values out of 1). The value obtained in 2) can be regarded as a measure for the disparity of the batches with respect to the skewness of the observation-wise empirical distributions.

For more than two batches: 1) for all possible pairs of batches: calculate the metric as described above; 2) calculate the weighted average of the values in 1) with weights proportional to the sum of the sample sizes in the two respective batches.

The variables are standardized before the calculation to make the metric independent of scale.

References

Shabalin, A. A., Tjelmeland, H., Fan, C., Perou, C. M., Nobel, A. B. (2008). Merging two gene-expression studies via cross-platform normalization. Bioinformatics 24(9):1154-1160, <10.1093/bioinformatics/btn083>.

Examples

# NOT RUN {
data(autism)

skewdiv(xba=X, batch=batch)

params <- ba(x=X, y=y, batch=batch, method = "ratiog")
Xadj <- params$xadj

skewdiv(xba=Xadj, batch=batch)

params <- ba(x=X, y=y, batch=batch, method = "combat")
Xadj <- params$xadj

skewdiv(xba=Xadj, batch=batch)
# }