[BioC] Re: flags?

Gordon Smyth smyth at wehi.edu.au
Wed Dec 31 05:24:54 MET 2003

At 01:01 PM 31/12/2003, Simon Melov wrote:
>when you assign zero weights to spots with flags, is this via the wtfun? 
>(i.e. as in the guide )
> > RG <- read.maimages(files,source="genepix",wt.fun=wtflags(0.1))
>or is there another way to specifically id certain types of flags in limma 
>(eg -50 vs -100)?

You can specify any weight function that you like, but you have to define 
it yourself. For example, if you wish to give zero weight to all flags less 
than -50 you could use

myfun <- function(x) as.numeric(x$Flags > -50.5)
RG <- read.maimages(files, source="genepix", wt.fun=myfun)



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