MC6_Methods: Load list of level 6 multiple-concentration flag methods
In GladiaTOX: R Package for Processing High Content Screening data

Description Usage Value Available Methods See Also

mc6_mthds returns a list of flag methods to be used during level 6 multiple-concentration processing.

1	mc6_mthds()

A list functions

More information about the level 6 multiple-concentration processing is available in the package vignette, "Pipeline_Overview."

row.dev.up: The row.dev.up flag looks at the individual point data, searching for row effects across an apid. To get flagged the point has to be greater than 3 standard deviations above the mean response for the plate, and the row mean must be greater than 3 standard deviations above the row means for the plate.
row.dev.dn: The row.dev.dn flag is identical to the row.dev.up flag, but identifies points falling in rows with decreased signals.
col.dev.up: The col.dev.up flag is identical to the row.dev.up flag, but identifies points falling in columns with increased signals.
col.dev.dn: The col.dev.up flag is identical to the row.dev.up flag, but identifies points falling in columns with decreased signals.
plate.flare: The plate.flare flag looks at the individual point data, searching for overly active regions across an apid. Intended for use in fluorometric assays that are read by a plate-reader that measures the plate as a whole, rather than measuring individual wells. For each well the flare value is calculated as a weighted mean a 5 well by 5 well box centered on the well where the weight given to each well in the box is the euclidian distance from the center well. The flag then identifies points with flare values greater than 3 standard deviations above the mean flare values for the plate.
plate.interlace: The plate.interlace flag is specific to one experimental design that plates chemicals from a 386 well chemical plate to a 1536 well assay plate. The flag looks for any chemical-plate affects, by looking for an increased signal in the wells originating from the same chemical plate.
rep.mismatch: The rep.mismatch flag is still in development and is not suggested for use at this time.
pintool: Deprecated. The pintool flag uses a complicated algorithm to look for signal potentially caused by residual in the pintool used to deliver the chemical to assay plates in some experimental designs. The gnls.lowconc is a faster and simpler way to identify where this problem may be driving the activity or hit-call.
singlept.hit.high: The singlept.hit.high flag identifies concentration series where the median response was greater than 3*bmad only at the highest tested concentration and the series had an active hit-call.
singlept.hit.mid: The singlept.hit.mid flag identifies concentration series where the median response was greater than 3*bmad at only one concentration (not the highest tested concentration) and the series had an active hit-call.
multipoint.neg: The multipoint.neg flag identifies concentration series with response medians greater than 3*bmad at multiple concentrations and an inactive hit-call.
gnls.lowconc: The gnls.lowconc flag identifies concentration series where the gain-loss model won, the gain AC50 is less than the minimum tested concentration, and the loss AC50 is less than the mean tested concentration.
noise: The noise flag attempts to identify noisy concentration series by flagging series where the root mean square error for the series is greater than the cutoff for the assay endpoint.
border.hit: The border.hit flag identifies active concentration series where the top parameter of the winning model was less than or equal to 1.2*cut-off or the the activity probablity was less than 0.9.
border.miss: The border.miss flag identifies inactive concentration series where either the Hill or gain-loss top parameter was greater than or equal to 0.8*cut-off and the activity probability was greater than 0.5.
overfit.hit: The overfit.hit flag recalculates the model winner after applying a small sample correction factor to the AIC values. If the hit-call would be changed after applying the small sample correction factor the series is flagged. Series with less than 5 concentrations where the hill model won and series with less than 7 concentrations where the gain-loss model won are automatically flagged.
efficacy.50: The efficacy.50 flag identifies concentration series with efficacy values (either the modeled top parameter for the winning model or the maximum median response) are less than 50. Intended for use with biochemical assays where one might expect at least a 50% change in real responses.