I would like to perform differential expressed Genes analysis of a NimbleGen data. I have dataset of 48 .pair files and 48 .calls files.

1. Can I perform DE genes analysis only with these data + ndf file without using oligo package? (my data contains single channel only 532 output)
2. I have read that oligo packages uses only xys files so I tried to transform my .pair data to xys data using theileria.org's create_xys_files.pl script under AHDW project. We have extracted X Y and Signal values from the .pair files and inserted Count column. In the Count column, we entered NA for missing values.

After we do this, read.xysfiles() gave us

All the XYS files must be of the same type.
Error : checkChipTypes(filenames, verbose:'nimblegen') is not TRUE.

So what is the true way of transforming pair data to xys.

Our pair files don't include header line somehow. I have seen that this header line contains some information? (which starts with # software=NimbleScan)

Please help me

Thank you in advance

Best Regards
Tunc