transform_Agilent_log: Log transform and offset of Agilent data.
In drmjc/microarrays: A collection of microarray and genomic helper code.

Description Usage Arguments Value Author(s)

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)

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

`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

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).

Mark Cowley, 2008-08-01

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