virtualArrayComBat: Removes batch effects from microarray derived expression...

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

Description

This is a modified version of the R script "ComBat.R" (see references). It is used to adjust for batch effects in microarray data. The modification is restricted to make the script accept expression matrices and data.frames instead of plain text files.

Usage

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virtualArrayComBat(expression_xls, sample_info_file, type = "txt", write = FALSE, covariates = "Batch", par.prior = TRUE, filter = FALSE, skip = 0, prior.plots = FALSE)

Arguments

expression_xls

The expression matrix to adjust.

sample_info_file

The sample information data.frame regarding batch contribution and possibly covariates.

type

The type of input; Defaults to "txt".

write

Write output to external file or provide new expression matrix.

covariates

Describe which Covariates to use in the process and which to dismiss. The default is to use only "Batch".

par.prior

Logical; set prior parameters or not; Use prespecified values for the variables ("TRUE") or start a priori ("FALSE").

filter

Filter for genes not present in a given percentage of the samples. Requires present/absent calls in the data. Can be either "FALSE" or a numeric between "0" and "1". Recommended is "0.8" or "FALSE".

skip

Columns to skip in the input "expression_xls" matrix.

prior.plots

Create quantile-quantile and kernel density plots including prior estimates to assess the quality of the estimation.

Value

Returns a matrix holding adjusted expression values.

Note

Original code by Johnson, WE, Rabinovic, A, and Li, C, made available in this package by Andreas Heider

Author(s)

Original author: Johnson, WE, Rabinovic, A, and Li, C (2007)

Modified by: Andreas Heider (2011)

References

Johnson, WE, Rabinovic, A, and Li, C (2007). Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics 8(1):118-127.

See Also

virtualArray-package, virtualArray.ExpressionSet, virtualArrayCompile

Examples

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virtualArray documentation built on Sept. 12, 2016, 6:10 a.m.