I have 23 .pair files from NimbleGen Drosophila melanogaster 12X135K Gene Expression Array with GEO accession number GSE100142. I want to process these in R and get a normalized expression matrix as output with samples in column and probes in the rows. Is there an R package for it?
Like Affymetrix .cel files could be processed using affy library's ReadAffy function to load the files and then rma function to normalize it. I need a similar code for .pair files. I figured HELP library could be used but I couldn't get it to properly run. I am new to R and processing NimbleGen files, please help in finding commands that will normalize .pair files from NimbleGen.