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Dear all,

I want to analyse some micrarray data from GEO datasets which employs the Nimblegen microarray, single label. I am completely new to R programming, and I have been trying to analyse the raw data using online tutorials. While I could find the commands for CEL/XYS files, I could not find any for pair files. I have a set of 12 pair files, 1 ncd and 1 ngd file. I have been trying to read the signal using the oligo package and go about further processing. Could anyone please help me out here?

Is there a way to convert pair to xys files, or is there a way one could directly read and annotate pair files? Since I am completely new to it, the appropriate commands would be helpful!

Thanks a ton in advance!

Have you tried the HELP package? Seems relevant.