I'm studying the Connectivity Map data and I'm wondering how probe sets are ordered for an instance. I read the following paragraph in help section of Connectivity Map (https://www.broadinstitute.org/cmap/help_topics_frames.jsp):
"[..] All average difference values from the treatment scan are scaled relative to those from its corresponding control using a linear-fit-on-P-call algorithm, giving scaled average difference values. In six-well batches, average difference values for the control are from a single scan. In ninety-six-well batches, the control expression values are the composite of the five or six control scans. Average difference values for each probe set are the arithmetic mean of the five or six individual average difference values for that probe set. A probe set is given a 'P' call if more than three of the individual confidence calls are 'P' for that probe set. Average difference (control) and scaled average difference (treatment) values less than a primary threshold value are set to that threshold value. Average difference (control) and scaled average difference (treatment) values less than a second, lower threshold value are set to that secondary threshold value.
A ratio value d and a secondary ratio value d ′ are then computed for each probe set p: [...]" d_p = t_p/c_p d_p' = t_p' /c_p'
I have not clear how the difference values from treatment scan are scaled relative to those from its corresponding control using a linear-fit-on-P-call algorithm (Is this sentence referred to probe set values or probes value (PM/MM)?) I would understand how the average difference for the control and the scaled average difference values for treatment are calculated in order to calculate the final value d. Finally, I would clarify how the threshold t and t' are set and the meaning of these threshold.
I really appreciate any help you can provide.
Thanks for availability.