PaGE_5.1 Documentation - the --design command

This applies only to two-channel data. In this case there are one of two possibilities:

• Direct Comparison Design: Two conditions are compared with one condition hybridized to one channel and the other condition hybridized to the other channel. The data for each array consists of (possibly normalized) ratios (one should never use the individual channels as one channel data).
• Reference Design: Two or more conditions are compared, but not directly to each other as in the Direct Comparison Design, instead they are each compared to a common reference. The data for each array consists of (possibly normalized) ratios, with the experimental channel in the numerator and the reference channel in the denominator.
  • Any gene is expected to have relatively constant abundance in the reference channel across all arrays.

This command takes one argument of type string, which must be R or D.

Example 1: Reference Design

> perl PaGE_5.1.6.pl --design R

Example 2: Direct Comparison Design

> perl PaGE_5.1.6.pl --design D