array2channel {limma}R Documentation

Convert Two-Color Targets File to One-Row-Per-Channel

Description

Convert a two-color targets from with one row per array to one with one row per channel.

Usage

array2channel(targets, channel.codes=c(1,2), channel.columns=list(Target=c("Cy3","Cy5")), grep=FALSE)

Arguments

targets data.frame with one row per array giving information about target samples associated covariates.
channel.codes numeric or character vector of length 2 giving codes for the channels
channel.columns named list of character vectors of length 2. Each entry gives a pair of names of columns in targets which contain channel-specific information. This pair of columns should be assembled into one column in the output.
grep logical, if TRUE then the column names are founding by greping, i.e., the actual column names need only contain the names given by channel.columns as substrings

Details

This function is used to convert the usual two-color representation of target information into a form suitable for single-channel analysis.

Value

data.frame with twice as many rows as targets. Any pair of columns named by channel.columns will now be one column.

Author(s)

Gordon Smyth

See Also

coerce,RGList,exprSet-method

An overview of methods for single channel analysis in limma is given by 6.SingleChannel.

Examples

targets <- data.frame(FileName=c("file1.gpr","file2.gpr"),Cy3=c("WT","KO"),Cy5=c("KO","WT"))
array2channel(targets)

[Package limma version 1.6.7 Index]