MC3_Methods: List of level 3 multiple-concentration normalization methods
In GladiaTOX: R Package for Processing High Content Screening data

Description Usage Details Value Available Methods Note See Also

mc3_mthds returns a list of normalization methods to be used during level 3 multiple-concentration processing.

1	mc3_mthds()

The functions contained in the list returned by mc3_mthds take 'aeids' (a numeric vector of aeid values) and returns a list of expressions to be executed in the mc3 (not exported) function environment. The functions are described here for reference purposes, The mc3_mthds function is not exported, nor is it intended for use.

All available methods are described in the Available Methods section, listed by the type of function and the function/method name.

A list of functions

The methods are broken into three types, based on what fields they define. Different methods are used to define "bval" (the baseline value), "pval" (the positive control value), and "resp" (the final response value).

Although it does not say so specifically in each description, all methods are applied by aeid.

More information about the level 3 multiple-concentration processing is available in the package vignette, "Pipeline_Overview."

bval Methods

bval.apid.nwlls.med: Calculate bval as the median of cval for wells with wllt equal to "n," by apid.
bval.apid.1owconc.med: Calculate bval as the median of cval for wells with wllt equal to "t" and cndx equal to 1 or 2, by apid.
bval.apid.twlls.med: Calculate bval as the median of cval for wells with wllt equal to "t," by apid.
bval.apid.tn.med: Calculate bval as the median of cval for wells with wllt equal to "t" or "n," by apid.
bval.apid.nwllslowconc.med: Calculate bval as the median of cval for wells with wllt equal to "n" or wells with wllt equal to "t" and cndx equal to 1 or 2, by apid.
bval.spid.lowconc.med: Calculate bval as the median of cval for wells with wllt equal to "t" and cndx equal to 1, 2, or 3, by spid.

pval Methods

pval.apid.pwlls.med: Calculate pval as the median of cval for wells with wllt equal to "p," by apid.
pval.apid.mwlls.med: Calculate pval as the median of cval for wells with wllt equal to "m," by apid.
pval.apid.medpcbyconc.max: First calculate the median of cval for wells with wllt equal to "p" or "c," by wllt, conc, and apid. Then calculate pval as the maximum of the calculated medians, by apid.
pval.apid.medpcbyconc.min: First calculate the median of cval for wells with wllt equal to "p" or "c," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.
pval.apid.medncbyconc.min: First calculate the median of cval for wells with wllt equal to "m" or "o," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.
pval.apid.pmv.min: First calculate the median of cval for wells with wllt equal to "p," "m," or "v," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.
pval.apid.pmv.max: First calculate the median of cval for wells with wllt equal to "p," "m," or "v," by wllt, conc, and apid. Then calculate pval as the maximum of the calculated medians, by apid.
pval.apid.f.max: First calculate the median of cval for wells with wllt equal to "f," by wllt, conc, and apid. Then calculate pval as the maximum of the calculated medians, by apid.
pval.apid.f.min: First calculate the median of cval for wells with wllt equal to "f," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.
pval.apid.p.max: First calculate the median of cval for wells with wllt equal to "p," by wllt, conc, and apid. Then calculate pval as the maximum of the calculated medians, by apid.
pval.apid.p.min: First calculate the median of cval for wells with wllt equal to "p," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.
pval.apid.v.min: First calculate the median of cval for wells with wllt equal to "v," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.
pval.zero: Define pval as 0.

resp Methods

resp.pc: Calculate resp as (cval - bval)/(pval - bval)*100.
resp.fc: Calculate resp as cval/bval.
resp.logfc: Calculate resp as cval - bval.
resp.log2: Take the logarithm of resp with base 2.
resp.mult25: Multiply resp by 25.
resp.scale.mad.log2fc: Multiply resp by the scale factor log2(1.2)/(3*bmad).
resp.scale.quant.log2fc: Determine the maximum response md where md = abs(1st centile - 50th centile) or abs(99th centile - 50th centile), whichever is greater. Scale the response such that 20 percent of md equals log2(1.2).
resp.multneg1: Multiply resp by -1.
resp.shiftneg.3bmad: Shift all resp values less than 3*bmad to 0.
resp.shiftneg.6bmad: Shift all resp values less than 6*bmad to 0.
resp.shiftneg.10bmad: Shift all resp values less than 10*bmad to 0.
resp.blineshift.3bmad.repi: Shift resp values with the blineShift function by repi, where the window (wndw) is 3*bmad.
resp.blineshift.50.repi: Shift resp values with the blineShift function by repi, where the window (wndw) is 50.
resp.blineshift.3bmad.spid: Shift resp values with the blineShift function by spid, where the window (wndw) is 3*bmad.
resp.blineshift.50.spid: Shift resp values with the blineShift function by spid, where the window (wndw) is 50.
none: Do no normalization; make resp equal to cval.