SC1_Methods: List of level 1 single-concentration normalization functions
In GladiaTOX: R Package for Processing High Content Screening data

Description Usage Details Value Available Methods Note See Also

sc1_mthds returns a list of functions to be used during level 1 single-concentration processing.

1	sc1_mthds()

The functions contained in the list returned by sc1_mthds return a list of expressions to be executed in the sc2 (not exported) function environment. The functions are described here for reference purposes, The sc1_mthds function is not exported, nor is it intended for use.

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

A list 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 acid.

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

bval Methods

bval.apid.nwlls.med: Calculate bval as the median of rval for wells with wllt equal to "n," by apid.
bval.apid.twlls.med: Calculate bval as the median of rval for wells with wllt equal to "t," by apid.
bval.apid.tn.med: Calculate bval as the median of rval for wells with wllt equal to "t" or "n," by apid.

pval Methods

pval.apid.pwlls.med: Calculate pval as the median of rval for wells with wllt equal to "p," by apid.
pval.apid.mwlls.med: Calculate pval as the median of rval for wells with wllt equal to "m," by apid.
pval.apid.medpcbyconc.max: First calculate the median of rval 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 rval 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 rval 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.zero: Define pval as 0.