Reads all files in Nimblegen pair format within the specified directory, returning log2 intensities of probes referenced by the supplied ndf data frame.
the directory containing the pair files to be read.
a data frame produced by
specifies the channel(s) to be read in - either
the number of columns of probes on the array - must be the same value as used in
Reads in intensities of all arrays contained within
path. The parameter
what determines which fluorescent channels are read, and how the are returned.
Cy5 return the log2 intensity of the specified single channel.
Cy5/Cy3 return the log2 ratio of the two channels.
Cy5andCy3 return the log2 intensity of both channels in separate columns of the matrix.
matrix of log2 intensites, with the same number of rows as the supplied
ndf and depending on the value of
what either one or two columns per array.
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# Not run # ## Read in the NDF file # ndfAll <- processNDF("080310_HG18_chr7RSFS_AS_ChIP.ndf") # ## Subset the NDF to only probes against chromosomes # ndf <- ndfAll[grep("^chr", ndfAll$chr),] # ## Read in a directory of pair files, returning both the Cy3 and Cy5 fluorescence in separate columns # arrayIntensities <- loadSampleDirectory("Arrays", ndf, what="Cy3andCy5") #
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