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.

Thank You

The oligo package is the only way I know of to process Nimblegen data, and it won't work with pair files, but instead wants the xls files. The differences between the two are outlined here.

You could hypothetically parse the .pair files to create xls files and then process using oligo, or you could look through the code for the HELP package to see how two-color data are handled and write code to handle one-color data. But the sample processing statement from the submitter indicates that these data were processed using quantile normalization and the RMA algorithm (using ArrayStar). Unless you want to do something completely different to preprocess the data, I would just use GEOquery to get the processed data (which apparently are not log transformed, so you should do that yourself). By far the most simple way to proceed is to use GEOquery.

I will say that the density plot of those data looks pretty crazy, being trimodal and all, but I have not had the opportunity to work with Nimblegen data, so maybe that's expected.