[BioC] text.to.search problem in read.maimages

[Erik Dopman]

Dear List:

I am running R v 2.4.1 and limma v 2.9.17, both of which were  
recently installed from older versions. Since making the update to  
newer versions, I am now unable to run my weight function in the  
read.maimages function. The error that I am receiving is:

Warning message:
the condition has length > 1 and only the first element will be used  
in: if (text.to.search != "") for (i in 1:ncn) {


Has anybody run into this problem before? My overly redundant filter  
function and scan statement is below.

Thanks,
Erik


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))
	}

RG <- read.maimages(targets, source="genepix", columns=list(Rf="F635  
Median",
	Gf="F532 Median", Rb="B635 Median", Gb="B532 Median"),
	other.columns=list("B635 SD", "B532 SD", "F635 Median - B635",
	"F532 Median - B532", "% > B635+2SD", "% > B532+2SD", "F635 % Sat.",
	"F532 % Sat.", "Dia.", "Ratio of Medians (635/532)", "Rgn Ratio  
(635/532)",
	"B635 Mean", "B635 Median", "B532 Mean", "B532 Median",
	"Median of Ratios (635/532)", "Sum of Medians (635/532)"), wt.fun =  
filter)