[BioC] R crashes on winXP with 2G memory

[Hao Liu]

Dear All:

I encountered this several times, could someone point out where the problem
is? I don't think it is the memory restriction or something...

I have 345 MAS5 results formated as: probeset_id, expression_value, PA_call
in 345 text file. I tried to combine them into one single file, but only
retain one probeset_ID column.

This is my commend:

Files<-list.files(pattern=".txt$");
Count<-0;
for(i in files) {x<-read.table(i, header=TRUE,sep="\t"); assign(print(i,
quote=FALSE),x);if(count==0){combined<-x;rm(x);count<-count+1;} else
{combined<-cbind(combined,x[,2:3]);rm(x);count<-count+1;}}

After processing over 200 files, the program crashes.

Is there a better way to get it done? And, for this large dataset, if I
don't want to use RMA -- which is easier to get using justrma, I am stuck
here...

Thanks
Hao