R to automate scatter plots

Hi R people!

I have a directory of .csv files I would like to make into objects  
then scatter plots. I have been having varying degrees of progress.  
I was able
make an object of all files, loop through it, and make a pdf of the  
last file I looped through. I kept renaming the pdf so instead of  
ending up with
27 pdfs I got one, with the data from the last file

I have been tweaking with it and now can't even make the data object  
and I am not sure why.

I am a bit brain dead at this point :)

I am new to R and have been programming in perl - but not all that  
long

Could you please have  al look at it..

here is the script I have been using

# source of this code below
#http://cran.r-project.org/doc/contrib/Lemon-kickstart/kr_scrpt.html

# store the current directory
initial.dir<-getwd()
# change to the new directory
setwd("/data/homes/ccpage/ngs/Argueso/Tophat/flocculated/cuffdiff/ 
fpkmgt")

# source of this code below
# https://stat.ethz.ch/pipermail/r-help/2008-March/158336.html


files <- Sys.glob("*.csv")  # get names of files to process
#result <- numeric(length(files))  # preallocate assuming single  
value from each file

for (i in seq_along(files)){
# want to give each object a unique name would like to use file[i]  
MINUS the .csv extention regex
#test<-files[i] # tried to use as variable to name each pdf this  
object is the name of last file in loop

  data <- read.csv(files[i])

# I want to name the pdf the same name as the object with a .pdf  
extention here I think it will be file[i].csv.pdf
# I don't know how to use regex	in R I could  
readLines(objectnames.txt)	and loop through those as well

   pdf("data.pdf")

   plot(data$fpkma,data$fpkmb, main="Scatter plot of  
data",xlab="FPKM of First Time Point",ylab="FPKM of Second Time  
Point")
   dev.off()
}

# change back to the original directory
setwd(initial.dir)
############################################################

the command I have been using :
R CMD BATCH /data/homes/ccpage/ngs/rscripts/test_for.R

The Rout

# source of this code below
#http://cran.r-project.org/doc/contrib/Lemon-kickstart/kr_scrpt.html

# store the current directory
initial.dir<-getwd()
# change to the new directory
setwd("/data/homes/ccpage/ngs/Argueso/Tophat/flocculated/cuffdiff/ 

fpkmgt")

# source of this code below
# https://stat.ethz.ch/pipermail/r-help/2008-March/158336.html

files <- Sys.glob("*.csv")  # get names of files to process
#result <- numeric(length(files))  # preallocate assuming single  

value from each file

for (i in seq_along(files)){

+ # want to give each object a unique name would like to use file[i]  
MINUS the .csv extention regex
+ #test<-files[i] # tried to use as variable to name each pdf this  
object is the name of last file
+
+    data <- read.csv(files[i])
+
+ # I want to name the pdf the same name as the object with a .pdf  
extention here I think it will be file[i].csv.pdf
+ # I don't know how to use regex in R I could  
readLines(objectnames.txt) and loop through those as well
+
+     pdf("data.pdf")
+     plot(data$fpkma,data$fpkmb,main="Scatter plot of  
data",xlab="FPKM of First Time Point",ylab="FPKM of Second Time  
Point")
+     dev.off()
+ }
Error in plot.window(...) : need finite 'xlim' values

Calls: plot -> plot.default -> localWindow -> plot.window
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
Execution halted

Thanks for any help!\