[R] computer out of memory when using sigpathway

[Martin Morgan]

On 05/19/2010 09:15 PM, ɽÖÐ³Ì wrote:
> Dear R users,
> 
> 
> 
> I am sorry to disturb you! But I really need your help for the usage
> of sigPathwy.

Please ask questions about Bioconductor packages on the Bioconductor
mailing list, as other Bioconductor users are the ones mostly likely to
have experience with this package.

  http://bioconductor.org/docs/mailList.html

Include the package maintainer in your email as they are in the best
position to provide informed advice.

  > packageDescription("sigPathways")$Maintainer

Include the output of sessionInfo() in your email, so that the specific
versions of R and packages are unambiguous.

  > sessionInfo()

Provide a minimal and self-contained example, so that those wishing to
help can easily reproduce your problem. This requires additional work on
your part, but will often reward by pointing out where the problem is.
Sending large attachments is NOT recommended; instead, use example data
from the package, from an appropriate experiment data package, or simulated.

When reporting an error, copy and paste the output of the relevant
section of your script. This provides additional clues to where exactly
a problem occurs.

After the error occurs, call

  > traceback()

to discover where during the computation the problem was.

Run

  > example(runSigPathway)

to see an example, and compare your input data to the input in the
example. For instance, is your 'yy' structured the same as 'G' in the
example?

Hope this leads to a solution,

Martin


> 
> 
> 
> 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")
> 
> 
> 
> ______________________________________________ R-help at 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 
> and provide commented, minimal, self-contained, reproducible code.
Rr

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793