[BioC] Re: flags?

[Gordon Smyth]

At 01:01 PM 31/12/2003, Simon Melov wrote:
>Gordon,
>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)?
>Thanks

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)

Gordon


>S.