computer out of memory when using sigpathway
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@-4089
Last seen 6.5 years ago
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="Frequenc y",main="") set.seed(1234) YANG <- runSigPathway(yy,20,500,Y,p,nsim=100,weightType="constant",ngr oup=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.tx t") YANG\$list.gPS[[1]] save.image("chr1_sig")
Microarray Annotation sigPathway Microarray Annotation sigPathway • 585 views