transform_Agilent_log: Log transform and offset of Agilent data.

Description Usage Arguments Value Author(s)

Description

Usually, >90% of the negative values are in [-8,0), with the remainder being < 8. This method adds 8 to all values, then hard thresholds the remaining values that are still negative to some small positive number (eg 1)

Usage

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  transform_Agilent_log(data, offset = 8, minVal = 1,
    base = 2)

Arguments

data

a matrix-like object of agilent data, or a list of agilent data with an element called ‘value’

offset

the first offset that is added to all values.

minVal

if any values are small than this minVal, then hard-threshold them to this minVal

base

the logarithm base. default=2 for log-base-2

Value

if a matrix-like object was passed into this method, then a log transformed matrix is returned. If a list was passed into this method, then the value and error will be logged (base 2).

Author(s)

Mark Cowley, 2008-08-01


drmjc/microarrays documentation built on May 15, 2019, 2:26 p.m.