correctBlanks: Subtract Blank Values

In raim/platexpress: Inspection and Analysis of Microbial Growth and Gene Expression Data

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

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 [e-mail]

See Also

adjustBase

Examples

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

raim/platexpress documentation built on Jan. 18, 2022, 1:41 p.m.