[BioC] within array normalization for one color agilent array.??

[Sean Davis]

On Fri, Feb 19, 2010 at 1:29 AM, neeraj rana <kushrn at gmail.com> wrote:
> hi,
>
> In the package Agi4x44PreProcess  I took the expression value as *MeanSigna*l,
> then by the method *BGandNorm,* the background subtraction and the
> normalization between the array is done.But the array should be normalized
> within the array also first.This the script what is given in
> Agi4x44PreProcess for normalization.I didnt find any option for within the
> array normalization.
>
>> ddNORM = BGandNorm(dd, BGmethod = "half", NORMmethod = "quantile",
> + foreground = "MeanSignal", background = "BGMedianSignal",
> + offset = 50, makePLOTpre = FALSE, makePLOTpost = FALSE)
>
> please help me out how can we do the normalization within the array before
> between the array normalization for one color agilent array.

For one-color arrays, it usually suffices to perform between-array
normalization.

Sean