array2channel {limma} | R Documentation |
Convert a two-color targets from with one row per array to one with one row per channel.
array2channel(targets, channel.codes=c(1,2), channel.columns=list(Target=c("Cy3","Cy5")), grep=FALSE)
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 grep ing, i.e., the actual column names need only contain the names given by channel.columns as substrings |
This function is used to convert the usual two-color representation of target information into a form suitable for single-channel analysis.
data.frame with twice as many rows as targets
.
Any pair of columns named by channel.columns
will now be one column.
Gordon Smyth
An overview of methods for single channel analysis in limma is given by 6.SingleChannel.
targets <- data.frame(FileName=c("file1.gpr","file2.gpr"),Cy3=c("WT","KO"),Cy5=c("KO","WT")) array2channel(targets)