The default output of HumanMethylation450 BeadChip compatible scanner systems consists of

• a SampleSheet.csv file and
• file directories named after the Chips Sentrix-ID containing two *.idat files per sample.

To use the files generated by the scanner system with ADMIRE, all file directories have to be compressed (e.g. by running tar -zcvf compressFileName.tar.gz folderToCompress).

ADMIRE can then be called with admire -c SampleSheet.csv -z compressFileName.tar.gz

Hint: ADMIRE can also read files ending on *.tar.gz, *.tgz or *.tbz2.