[BioC] Background Measurements

[Jean Yee Hwa Yang]

Hi Jason,

> having looked at most of the documentation I was wondering if it is 
> possible to exclude background information from marrayInput  and/or 
> subsequent normalisation procedures,
> if so what the options would be ?
> read.marrayRaw currently needs name.Gb & name.Rb ???? which is data we 
> would like to exclude on occasions

Yes, that is possible.  There is two ways of doing it.

1) Either use read.marrayRaw and don't put any argument for name.Gb and
name.Rb
e.g. read.marrayRaw("test.gpr", name.Gf="F532 Mean", name.Rf="F635 Mean")

2) If you are using data from GenePix or Spot you can use the function
read.GenePix and read.Spot which has a few defaults argument.  In those
cases you can set the background to zero at a later stage:
e.g. 
y <- read.GenePix("test.gpr")
maGb(test) <- matrix(0,0,0)
maRb(test) <- matrix(0,0,0)

The rest of the normalization and anlaysis plot will then be perform with
no background subtraction.

Cheers

Jean