targetsA2C(targets, channel.codes = c(1,2), channel.columns = list(Target=c("Cy3","Cy5")), grep = FALSE)targets which contain channel-specific information.
This pair of columns should be assembled into one column in the output.TRUE then the channel column names are found by greping, i.e., the actual column names need only contain the names given by channel.columns as substringstargets.
Any pair of columns named by channel.columns will now be one column.
targets dataframe holds information about the RNA samples used as targets in the microarray experiment.
It is often read from a file using readTargets.
This function is used to convert the dataframe from an array-orientated format with one row for each array and two columns for the two channels into a channel-orientated format with one row for each individual channel observations.
In statistical terms, the first format treats the arrays as cases and treats the channels as repeated measurements.
The second format treats the individual channel observations as cases.
The second format may be more appropriate if the data is to be analyzed in terms of individual log-intensities.
targetsA2C is used by the coerce method from RGList to ExpressionSet in the convert package.An overview of methods for single channel analysis in limma is given by 07.SingleChannel.
targets <- data.frame(FileName=c("file1.gpr","file2.gpr"),Cy3=c("WT","KO"),Cy5=c("KO","WT"))
targetsA2C(targets)
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