[BioC] problem with read.maimages wt.fun
gb606342000
gb606342000 at yahoo.com
Thu Sep 3 21:09:59 CEST 2009
Dear list member,
I am having problem using filtering data using read.maimages and wt.fun (the files are genepix .gpr).
I HAVE THIS FILTER:
filter <- function(x) {
ifforeground <- (
(x[,"% > B635+2SD"] > 70 | x[,"% > B532+2SD"] > 70) &
(x[,"F635 Median - B635"] > 4 * x[,"B635 SD"]) &
(x[,"F532 Median - B532"] > 4 * x[,"B532 SD"]) &
x[,"F635 % Sat."] < 30 & x[,"F532 % Sat."] < 30 &
x[,"Dia."] > 60 &
(x[,"B635 Mean"] < (1.2 * x[,"B635 Median"]) &
x[,"B532 Mean"] < (1.2 * x[,"B532 Median"])) &
(x[,"Ratio of Medians (635/532)"] < (1.2 * x[,"Rgn
Ratio
(635/532)"]) |
x[,"Ratio of Medians (635/532)"] > (0.8 * x[,"Rgn
Ratio
(635/532)"])) &
x[,"Sum of Medians (635/532)"] > 1000
)
ifnotflag <- x$Flags >= 0
return(as.numeric(ifnotflag & ifforeground))
}
WHEN I RUN THE SCRIPT BELOW, THERE IS NO PROBLEM:
RG1 = read.maimages(targets, source="genepix",
other.columns=list("% > B635+2SD", "% > B532+2SD","Flags"))
WHEN I ADD wt.fun WITH THE ABOVE filter I GET AN ERROR MESSENGE:
RG1 = read.maimages(targets, source="genepix",
other.columns=list("% > B635+2SD", "% > B532+2SD","Flags"), wt.fun=filter)
Error in gsub("\\.", "\\\\.", x) :
input string 1 is invalid in this locale
+
Does anyone could help me figure out what is going on?
Thanks.
Giovani
> sessionInfo()
R version 2.9.2 (2009-08-24)
i386-apple-darwin8.11.1
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] marray_1.22.0 limma_2.18.2
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