[BioC] How to use subset in maNorm() function of marrayNorm

[michael watson (IAH-C)]

Hi

Does anyone have a quick example of how to use the "subset" parameter of the maNorm function in marrayNorm?

The documentation states:

maNorm(mbatch, norm=c("printTipLoess", "none", "median", "loess",
"twoD", "scalePrintTipMAD"), subset=TRUE, span=0.4, Mloc=TRUE,
Mscale=TRUE, echo=FALSE, ...)

subset: A logical or numeric vector indicating the subset of points used to compute the normalization values.

But HOW? ;-) What form of vector?  is it:

i) the name of a slot, full of 1's and 0's, in the marrayRaw object indicating whether to use that row of data in the normalisation (1) or not (0)?

ii) an independent vector full of 1's and 0's, in the SAME order as the data in the marrayRaw object, indicating which rows of data to use in the normalisation?

iii) a vector of indices of the rows within the marrayRaw object to use for normalisation (E.g. subset=(3,5,7) means use only rows 3, 5 and 7 for the normalisation)?

iv) some other way, perhaps to do with marrayInfo..??

For background, the data I have has been quality controlled OUTSIDE of R, such that every spot on every array has a value of 1 or 0 depending on whether we thing the spot is a good spot (1) or a bad spot (0).  We only want to use good spots to calculate our normalisation factors.  

I'm sorry if I am being dumb but some good examples of how to use subset and marrayInfo would be really very useful :-D

Thanks in advance for your help :-D

Mick