[R] computer out of memory when using sigpathway

[山中程]

Dear R users,
 
 
 
I am sorry to disturb you! But I really need your help for the usage of sigPathwy.
 
 
 
Actually, I want a sliding window analysis for possible chromosome expression pattern mining. My research microorganism is a plant pathogen, Gibberella zeae, and I first used SAS to divide locus number with 10, 20, 30, or 40 on the fungal chromosome according to their location. I really want to see whether among the continual 10, 20, 30, or 40 locus has some expression pattern that different from rest genes. Because I know sigPathway (R package, pathway analysis with microarray data) can do this kind of job. What I use SAS to do is to subset locus in arbitrary genes numbers, such as 10, 20, 30, 40, or so on, and I hope to use sigPathway to analysis whether these genes chromosome location have effect on its gene expression. 
 
When I used sigpathway to analyze my microarray data, it made my computer out of memory. I have tried the following R codes in several computer, but it always the same, even if it computed more than one day, it can not get any results. I also try to use memory.limit(size=NA), it dosen't work too.My computer is a cor duo 2G DDR2, I think it is large enough for my job. Would you please point out my problem and give me some suggestions? Thank you very much.
 
I attach my microarray data and R codes in the attachment, and I hope you can have a look. 
 
 
 
 #the following code is for annotation list initiation.
 
       
 
 setwd("C:/analysis data and codes")
 
       x <- read.table("chr1.txt",header=FALSE,sep="\t")
 
       attach(x)
 
       x$group <- paste(V2,V3,sep="_")
 
       group <- x$group
 
       y <- data.frame(group,V2,V3,V4)
 
       xx <- as.list(group)
 
       xx <- xx[!is.na(xx)]
 
       xx <- unlist(xx)
 
       xxUnique <- unique(xx)
 
       yy <- vector("list",length(xxUnique))
 
       for(i in 1:length(yy))
 
       {
 
        MT <- "MT_lab"
 
        yy[[i]] <- list(src=MT,title=xxUnique[i],probes=as.character(y[group==xxUnique[i],]$V4))
 
        }
 
  
 
  
 
#the following code is for sigpathway analysis.
 
   
 
library(sigPathway)
 
YANG <- read.table("All microarray MT_LAB.txt",header=T,sep="\t")
 
attach(YANG)
 
Y <- data.frame(TF134_1_3DAK,TF134_2_3DAK,WT1_3DAK,WT2_3DAK,row.names=locus_no)
 
p <- c("1_trt","1_trt","0_norm","0_norm")
 
statList <- calcTStatFast(Y,p,ngroups=2)
 
hist(statList$pval,breaks=seq(0,1,0.025),xlab="p-value",ylab="Frequency",main="")
 
set.seed(1234)
 
YANG <- runSigPathway(yy,20,500,Y,p,nsim=100,weightType="constant",ngroup=2,npath=10,verbose=F,allpathway=F,alwaysUseRandomPerm=F)
 
#write.table(YANG$df.pathways[1:25, ])
 
write.table(YANG$df.pathways[1:25,],quote=F,sep="\t",file="chr1_sig.txt")
 
YANG$list.gPS[[1]] 
 
save.image("chr1_sig")