MC6_Methods: Load list of level 6 multiple-concentration flag methods
In pmpsa-hpc/GladiaTOX: R Package for Processing High Content Screening data
MC6_Methods R Documentation
Load list of level 6 multiple-concentration flag methods
Description
mc6_mthds returns a list of flag methods to be used
during level 6 multiple-concentration processing.
Usage
mc6_mthds()
Value
A list functions
Available Methods
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.
See Also
mc6, Method functions to query what
methods get applied to each aeid
pmpsa-hpc/GladiaTOX documentation built on Sept. 1, 2023, 5:52 p.m.
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| MC6_Methods | R Documentation |
Load list of level 6 multiple-concentration flag methods
Description
mc6_mthds returns a list of flag methods to be used
during level 6 multiple-concentration processing.
Usage
mc6_mthds()
Value
A list functions
Available Methods
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.
See Also
mc6, Method functions to query what
methods get applied to each aeid
R Package Documentation
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