[BioC] Weight functions for Agilent chips (limma)

[Malard, Joel M]

Hi Giovanni,
 
Sorry, being new to R programs, it took me some time to parse your own.
 
Could something of the sort be useful to you?
 
wtAgilent.mRGOLFilter <- function(qta) {
    mapply(min,1-qta[,"gIsFeatNonUnifOL"],1-qta[,"gIsFeatNonUnifOL"],
                  1-qta[,"gIsBGNonUnifOL"],1-qta[,"gIsBGNonUnifOL"],
                  1-qta[,"gIsFeatPopnOL"],1-qta[,"gIsFeatPopnOL"],
                  1-qta[,"gIsBGPopnOL"],1-qta[,"gIsBGPopnOL"])
    }

I don't see (visually) much difference (for this data set) between this
last filter and the previous
 
wtAgilent.mRGFilter <- function(qta) {
mapply(min,qta[,"gIsPosAndSignif"],qta[,"rIsPosAndSignif"]) }

best regards,
 
Joel
 
P.S. For completeness sake, the Agilent manual describes 8 0/1 variables
related to outliers: 
 
"gIsFeatNonUnifOL" and "rIsFeatNonUnifOL" :
    a value of 1 indicates Feature is a non-uniformity outlier in g(r)
Boolean flag indicating 
    if a feature is a NonUniformity Outlier or not. A feature is
non-uniform if the pixel noise 
    of feature exceeds a threshold established for a "uniform" feature.
 
"gIsBGNonUnifOL" and " rIsBGNonUnifOL" : 
    a value of 1 indicates Local background is a non-uniformity outlier
in g(r).
 
"gIsFeatPopnOL" and " rIsFeatPopnOL" : 
    a value of 1 indicates Feature is a population outlier in g(r).
Probes with replicate features on 
    a microarray are examined using population statistics. A feature is
a population outlier if its 
    signal is less than a lower threshold or exceeds an upper threshold
determined using the 
    interquartile range (i.e., IQR) of the population.
 
"gIsBGPopnOL" and "rIsBGPopnOL" : 
    a value of 1 indicates local background is a population outlier in
g(r).
 
> Hi Joel,
> actually, I was trying to use the 8 outlier fields (columns AZ-BG of
the Agilent output file) in a way similar to the 'flag' fields of other
platfoms...
> So, I started with 
> mywtfun <- function(exclude.flags=c(1,2,3)) function(obj)
> 1-(obj$rIsBGPopnOL %in% exclude.flags)
> and thenRG <-read.maimages(...blabla... wt.fun=mywtfun(c(1)))
> 
> and maybe there's a way to include the other fields as well....
> Any other ideas?
> 
> Cheers
> Giovanni



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