SCAN_TwoColor: Single-Channel Array Normalization (SCAN) for Agilent...

Description Usage Arguments Value Note Author(s) References Examples

View source: R/TwoColor.R

Description

This function is used to normalize Agilent two-color expression microarrays via the SCAN method.

Usage

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SCAN_TwoColor(inFilePattern, outFilePath = NA, batchFilePath = NA, verbose = TRUE)

Arguments

inFilePattern

Absolute or relative path to the input file to be processed. To process multiple files, wildcard characters can be used (e.g., "*.txt"). Alternatively, a Gene Expression Omnibus identifier (e.g., GSE39655 or GSM1072833) can be specified. This is the only required parameter.

outFilePath

Absolute or relative path where the output file will be saved. This is optional.

batchFilePath

Absolute or relative path to a tab-separated text file that indicates batch (and optionally, covariate information) for each sample. Optional.

verbose

Whether to output more detailed status information as files are normalized. Default is TRUE.

Value

A list is returned, containing two elements: a matrix containing normalized data values and a vector of probe names that correspond to each row of the matrix. The matrix will contain two columns—one corresponding to each channel—for each sample. When the array design contains duplicate probe names (this is common for control probes), the vector of probe names will also contain duplicates.

Note

If a Gene Expression Omnibus (GEO) identifier is specified for the inFilePattern parameter, an attempt will be made to download the sample(s) directly from GEO. If a study identifier (e.g., GSE39655) is specified, all CEL files from that study will be downloaded. If a sample identifier (e.g., GSM1072833) is specified, only that sample will be downloaded.

The batchFilePath parameter provides a convenient way to adjust the data for batch effects. It invokes the ComBat function within the sva package. Please see that package for additional details about how batch adjusting is performed. Batch adjusting is performed after values have been SCAN normalized.

Author(s)

Stephen R. Piccolo

References

Piccolo SR, Sun Y, Campbell JD, Lenburg ME, Bild AH, and Johnson WE. A single-sample microarray normalization method to facilitate personalized-medicine workflows. Genomics, 2012, 100:6, pp. 337-344.

Examples

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## Not run: 
# Normalize a file from GEO and save output to a file
result = SCAN_TwoColor("GSM1072833", "output_file.txt")

## End(Not run)

Bioconductor-mirror/SCAN.UPC documentation built on June 1, 2017, 1:13 a.m.