Sorry, the nasty for (min... loop is probably easier to read like this:

for (m in 1:8){
    for (n in 1:12){
        p<- 3*q; x.array[m,n] <- mean(as.matrix(x[(p-2):p,2:4])); q <- q+1;
if (n == 1){
            z<-3*m; x.blank2[(z-2):z,]<-as.matrix(x[(p-2):p,2:4])
        }; if (n==11){
            z<-3*m; x.nodrug2[(z-2):z,1:3]<-as.matrix(x[(p-2):p,2:4])
        }; if (n==12){
            z<-3*m; x.nodrug2[(z-2):z,4:6]<-as.matrix(x[(p-2):p,2:4])
        }
    }
}

 Richard

2009/12/11 Richard Thompson <bawan03@googlemail.com>

> Ista,
>
> Here is the full code:
>
>
> file<-read.table(file="input_file.txt",sep="\t")[,c(1,3:5)]
> file.rows<- c(nrow(file)/288)
> full.array <- array(0,dim=c(8,file.rows,12))
>
> cellnames <- rep("A",file.rows)
> barcodes <- rep("A",file.rows)
> t <- rep("A",file.rows)
> t11 <- rep("A",file.rows)
> cv <- rep("A",file.rows)
>
>
> for (k in 1:file.rows){
>
> plate<- file[(((k-1)*288)+1),1]
>
> barcodes[k] <- levels(plate)[plate]
>
> l <- k*288
> a <- l-287
> x<-file[a:l,]
> x.array<-matrix(0,ncol=12,nrow=8)
> n.array<-matrix(0,ncol=12,nrow=8)
> x.blank2 <- matrix(0,ncol=3,nrow=24)
> x.nodrug2 <- matrix(0,ncol=6,nrow=24)
> value <- data.frame(conc=0,fluor=2)
>
> # reformat (mean) input data into 96 well format
> q<-1
> for (m in 1:8){ for (n in 1:12){ p<- 3*q; x.array[m,n] <-
> mean(as.matrix(x[(p-2):p,2:4])); q <- q+1; if (n == 1){z<-3*m;
> x.blank2[(z-2):z,]<-as.matrix(x[(p-2):p,2:4])}; if
> (n==11){z<-3*m;x.nodrug2[(z-2):z,1:3]<-as.matrix(x[(p-2):p,2:4])}; if
> (n==12){z<-3*m; x.nodrug2[(z-2):z,4:6]<-as.matrix(x[(p-2):p,2:4])}}}
> x.blank<-c(x.blank2[,1],x.blank2[,3],x.blank2[,2])
>
> x.nodrug
> <-c(x.nodrug2[,1],x.nodrug2[,2],x.nodrug2[,3],x.nodrug2[,4],x.nodrug2[,5],x.nodrug2[,6])
> x.nodrug11 <-c(x.nodrug2[,1],x.nodrug2[,2],x.nodrug2[,3])
>
> # calculate output values
>
>
> cv[k] <- 100*(sd(x.blank)/mean(x.blank))
> t[k] <-
> (mean(x.nodrug)-mean(x.blank))/sqrt(((sd(x.nodrug)^2)/8)+((sd(x.blank)^2)/16))
> t11[k] <-
> (sqrt(8)*(mean(x.nodrug11)-mean(x.blank)))/sqrt(sd(x.nodrug11)^2+sd(x.blank)^2)
>
> }
>
>
> all.data
> <-data.frame(barcodes,t=format(as.numeric(t),digits=3),t11=format(as.numeric(t11),digits=3),cv=format(as.numeric(cv),digits=3))
> #write(format(t,digits=6), file= "R_drug_plot.log",append=TRUE,sep="\t")
>
> write.table(all.data, file=
> "R_drug_plot.log",append=TRUE,sep="\t",row.names=FALSE)
>
> When I first tried the mail list wouldn't let me send it as it contains the
> word "drug" too many times! so I only included the problematic parts.
> Rich
>
> 2009/12/11 Ista Zahn <istazahn@gmail.com>
>
> The lack of a reproducible example is a bigger problem than any lack
>> of clarity of the explanation.
>>
>> -Ista
>>
>> On Fri, Dec 11, 2009 at 2:08 AM,  <bawan03@googlemail.com> wrote:
>> > Apologies,
>> > I didn't explain this clearly. The Rscript is called by a perl script,
>> which creates "input_file.txt" by inserting 288 lines of (reformatted) data
>> for each data file in the directory.  So the Rscript will (and is doing) run
>> the loop a number of times equal to the number of files the perl script read
>> in. The problem is that it should only create the data.frame and write to
>> the file after the last iteration, but it's (creating and)writing the
>> complete data.frame every iteration.
>> > Sent using BlackBerry® from Orange
>> >
>> > -----Original Message-----
>> > From: jim holtman <jholtman@gmail.com>
>> > Date: Thu, 10 Dec 2009 18:00:54
>> > To: biscuit<bawan03@googlemail.com>
>> > Cc: <r-help@r-project.org>
>> > Subject: Re: [R] incorrect multiple outputs
>> >
>> > If I rad you code right, file.rows is equal to 1 and your 'for' loop
>> will
>> > only iterate once.  Is that what you were expecting?
>> >
>> > No reproducible code provided, so that is my best guess.
>> >
>> >>file.rows<- c(nrow(file)/288)  # "input_file.txt" contains 288
>> reformatted
>> > lines for each original data file
>> > ...
>> >>for (k in 1:file.rows){  # iterates code for each 288 line block of
>> > "input_file.txt"
>> > ...
>> >
>> > On Thu, Dec 10, 2009 at 11:39 AM, biscuit <bawan03@googlemail.com>
>> wrote:
>> >
>> >>
>> >> HI,
>> >> I'm having trouble with a piece of Rscript which keeps outputting
>> >> incorrectly. it's something like this: the code reads in from a file
>> which
>> >> contains (reformated) input
>> >>
>> >> >file<-read.table(file="input_file.txt",sep="\t")[,c(1,3:5)]
>> >> >
>> >> >file.rows<- c(nrow(file)/288)  # "input_file.txt" contains 288
>> reformatted
>> >> lines for each original data file
>> >> ...
>> >> >for (k in 1:file.rows){  # iterates code for each 288 line block of
>> >> "input_file.txt"
>> >> ...
>> >> >cv[k] <- 100*(sd(x.blank)/mean(x.blank))
>> >> >t[k] <-
>> >>
>> (mean(x.note)-mean(x.blank))/sqrt(((sd(x.note)^2)/8)+((sd(x.blank)^2)/16))
>> >> >t11[k] <-
>> >>
>> (sqrt(8)*(mean(x.note11)-mean(x.blank)))/sqrt(sd(x.note11)^2+sd(x.blank)^2)
>> >> >}
>> >> >
>> >>
>> >>
>> >all.data<-data.frame(barcodes,t=format(as.numeric(t),digits=3),t11=format(as.numeric(t11),digits=3),cv=format(as.numeric(cv),digits=3))
>> >> >write.table(all.data, file=
>> >> "R_drug_plot.log",append=TRUE,sep="\t",row.names=FALSE)
>> >>
>> >> this all works correctly except that I believed it would output to file
>> >> after completing the loop, instead it's writing to file every
>> iteration. so
>> >> the output file looks like:
>> >>
>> >> headers
>> >> a1
>> >> headers
>> >> a1
>> >> a2
>> >> headers
>> >> a1
>> >> a2
>> >> a3
>> >> ...
>> >>
>> >> I have checked the missing sections of code and can confirm there are
>> no
>> >> missing/additional brackets. Has anyone any idea why this is happening
>> and
>> >> what I can do about it?
>> >> --
>> >> View this message in context:
>> >> http://n4.nabble.com/incorrect-multiple-outputs-tp957192p957192.html
>> >> Sent from the R help mailing list archive at Nabble.com.
>> >>
>> >> ______________________________________________
>> >> R-help@r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/r-help
>> >> PLEASE do read the posting guide
>> >> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
>> <http://www.r-project.org/posting-guide.html>
>> >> and provide commented, minimal, self-contained, reproducible code.
>> >>
>> >
>> >
>> >
>> > --
>> > Jim Holtman
>> > Cincinnati, OH
>> > +1 513 646 9390
>> >
>> > What is the problem that you are trying to solve?
>> >
>> >
>> >        [[alternative HTML version deleted]]
>> >
>> >
>> > ______________________________________________
>> > R-help@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
>> > and provide commented, minimal, self-contained, reproducible code.
>> >
>> >
>>
>>
>>
>> --
>> Ista Zahn
>> Graduate student
>> University of Rochester
>> Department of Clinical and Social Psychology
>> http://yourpsyche.org
>>
>
>

	[[alternative HTML version deleted]]


