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

[Gordon Smyth]

Dear Erik,

BTW, are you sure this is good filter? I corrected the two incorrect 
column names in your filter() function, then used it to read in a set 
of GenePix data that I have. I found that your function filtered out 
80% of the data values, even though the data quality is excellent and 
most of the genes are expressed. Why would you want to throw out 80% 
of your data?

Best wishes
Gordon

>[BioC] text.to.search problem in read.maimages
>Erik Dopman ebd5 at cornell.edu
>Wed Apr 25 16:20:21 CEST 2007
>
>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)