correctBlanks: Subtract Blank Values

Description Usage Arguments Author(s) See Also Examples

View source: R/platereader.R

Description

The function subtracts values from "blank" wells. Optionally this can be done in bins over time (or the current x-axis value) to account for time-dependent blanks. E.g. fluorescence blanks from LB medium sometimes show time-dependence, perhaps due to light-dependent degradation of LB fluorescence. Separate blanks for each condition can be used via the by option, to be used the same way as in getGroups.

Usage

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correctBlanks(data, plate, type = "median", by, yids, xid, max.xid,
  mbins = 1, base, verb = TRUE, ...)

Arguments

data

the plate data list to be blank-corrected

plate

the plate layout where column "blanks" indicates which wells are to be treated as blanks

type

calculation of blank values from multiple time-points and wells; "median", "mean" or "ci95", where the latter subtracts the mean minus the 95% confidence interval to avoid blanked values below 0

by

a list of column IDs of the plate layout; separate blank correction will be attempted for groups in these columns; each group must have at least one specified blank associated

yids

IDs of the data which should be blank-corrected, all will be blanked if missing

xid

ID of the x-axis data to be used, if blanked along x-axis, set by mbins>1

max.xid

the maximal x-axis value where blanks should be used

mbins

the number of bins the x-axis is to be divided, if blanked along the x-axis, see xid

base

optional minimal value; all values will be raised by the same amount using the function adjustBase

verb

issued progress messages and info

...

further arguments to adjustBase

Author(s)

Rainer Machne [email protected]

See Also

adjustBase

Examples

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data(ap12)
data <- correctBlanks(data=ap12data, plate=ap12plate, by="strain")

raim/platexpress documentation built on Nov. 9, 2018, 5:38 p.m.