Hi Gordon,

I have read some of your answers regarding this issue but it does not answer mine. I have 5 separate image output files from Scanalyze (not one of the output listed in Limma). For each file, one of the column named FLAG contains the flagged values of 1 if bad and 0 if good. Can you please help me, how can I exclude these spots from the analysis.

The following commands helped me to read each file saved ast text (tab delimiter)
> filenames <- c("gp1.dat","gp2.dat","gp3.dat","gp4.dat","gp5.dat")
> RG <- read.maimages(filenames,annotation="My_spot_labels",
columns=list(Rf="CH1I",Gf="CH2I",Rb="CH1B",Gb="CH2B"))
 These are the notation in Scanalyze.

I have used one function in the archive and got the following error
 > mywtfun <- function(exclude.flags=c(1,2,3)) function(obj) 1-(obj$Flag %in% 
+ exclude.flags)
> RG <- read.maimages(filenames,annotation="My_spot_labels", columns=list(Rf="CH1I",Gf="CH2I",Rb="CH1B",Gb="CH2B"), wt.fun=mywtfun(c(1)))
Error in "[<-"(`*tmp*`, , i, value = numeric(0)) : 
        nothing to replace with

Thank you so much for your help.
Yolande



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