search for: pmon

Dear R Users, In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best: bgcorrect.metod = rma rma2 mas normalize.method = qspline quantiles loess pmcorrect.method = pmonly subtractmm mas summary.method = liwong avgdiff medianpolish mas There are many options within each method. I would appreciate a hint on the best combination. Thank you very much in advance. Roger Roger L. Vallejo, Ph.D. Computational Biologist & Geneticist U.S. Department of Agriculture,...

...ocessing (SMP) OS version: SuSe 8 SP3a CPU: 8 Memory: 64GB The codes are as follows: > Data <- ReadAffy(filenames = paste(HOME, "CelData/", fname, sep="")) > eset <- expresso(Data, normalize.method="invariantset", bg.correct=FALSE, pmc\ orrect.method="pmonly", summary.method="liwong") normalization: invariantset PM/MM correction : pmonly expression values: liwong normalizing...Error: cannot allocate vector of size 594075 Kb > gc() used (Mb) gc trigger (Mb) Ncells 797971 21.4 1710298 45.7 Vcells 76716794 585.4...

...t;")) > mem.limits() nsize vsize NA NA > gc() used (Mb) gc trigger (Mb) Ncells 530216 14.2 899071 24.1 Vcells 76196137 581.4 243983468 1861.5 > eset <- expresso(Data, normalize.method="invariantset", bg.correct=FALSE, pmc\ orrect.method="pmonly", summary.method="liwong") normalization: invariantset PM/MM correction : pmonly expression values: liwong normalizing...Error: cannot allocate vector of size 594075 Kb > gc() used (Mb) gc trigger (Mb) Ncells 797983 21.4 1710298 45.7 Vcells 76716811 585.4...

Hi When I'm using clang 3.1 with the isysroot argument, it doesn't seem to pick up header files from the directory I'm passing through the command line: > $ clang -isysroot/myownheaders -v foo.c -c -o foo.o > clang version 3.1 (tags/RELEASE_31/final) > Target: i386-pc-linux-gnu > Thread model: posix > "/usr/bin/clang" -cc1 -triple i386-pc-linux-gnu -emit-obj

...xt", header = TRUE, row.names = 2) pData(pd) #### load a <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose = TRUE) #### normalize x <- expresso(a, bg.correct = FALSE, normalize.method = "vsn", normalize.param = list(subsample = 1000), pmcorrect.method = "pmonly", summary.method = "medianpolish") ### genes with highest variation library(hgu133plus2.db) rsd <- apply(exprs(x), 1, sd) sel <- order(rsd, decreasing = TRUE)[1:250] u<-mget(row.names(exprs(x)[sel,]),hgu133plus2SYMBOL) heatmap(exprs(x)[sel, ], labRow=u) ### in this case...

On 03/04/2012 02:32 PM, Harel Cain wrote: > Thanks, but I'm not sure I understand. I see no such flag in clang 2.9 > nor couldn't I find any mention of it. What does it do? It's called -mllvm. You can use it like this. clang -mllvm -vectorize ... Cheers Tobi

...cess. I might be missing something. For example I have a shared/dynamic library which contains LLVM passes. I used to invoke them with llvmc like this: >>*llvmc mycode.c -o mycode.o -c -opt -Wo,=-load,libFoo.dylib,-Foo* Can this style of optimization be executed using -mllvm argument? Thx, PMon On Sun, Mar 4, 2012 at 3:48 PM, Tobias Grosser <tobias at grosser.es> wrote: > On 03/04/2012 02:32 PM, Harel Cain wrote: > > Thanks, but I'm not sure I understand. I see no such flag in clang 2.9 > > nor couldn't I find any mention of it. What does it do? > > I...

...ember/021136.html), isn't it related? > From: Joerg Sonnenberger <joerg at britannica.bec.de> > Date: Wed, Aug 29, 2012 at 4:03 PM > Subject: Re: [LLVMdev] Correct usage of isysroot argument > To: llvmdev at cs.uiuc.edu > > > On Wed, Aug 29, 2012 at 03:54:47PM +0300, pmon mail wrote: >> When I'm using clang 3.1 with the isysroot argument, it doesn't seem >> to pick up header files from the directory I'm passing through the >> command line: >> >> > $ clang -isysroot/myownheaders -v foo.c -c -o foo.o > > This means th...

...Affy()") 'Calculating RMA expression values... x.EvaluateNoReturn("eset <- expresso(data, bgcorrect.method=" + Chr(34) + "rma" + Chr(34) + ", normalize.method=" + Chr(34) + "quantiles" + Chr(34) + ", pmcorrect.method=" + Chr(34) + "pmonly" + Chr(34) + ", summary.method=" + Chr(34) + "avgdiff" + Chr(34) + ")") 'Writng output data x.EvaluateNoReturn("write.exprs(eset,file=" + Chr(34) + "output.txt" + Chr(34) + ")") x.Close() ------ The "Close()" command...

...1 OS: OS Tiger Submission from: (NULL) (65.93.158.117) I am trying to analyze microarray data of 42 human arrays. I typed in the following instructions: library(affy) Data <-ReadAffy() eset <- expresso(Data, normalize.method="invariantset", bg.correct=FALSE, pmcorrect.method="pmonly",summary.method="liwong") And I get some sort of memory error that crashes the R program. Specifically it states: R(1763) malloc: *** vm_allocate(size=346857472) failed (error code=3) R(1763) malloc: *** error: can't allocate region R(1763) malloc: *** set a breakpoint in szo...

Thanks, but I'm not sure I understand. I see no such flag in clang 2.9 nor couldn't I find any mention of it. What does it do? Harel Cain On Sun, Mar 4, 2012 at 15:03, Anton Korobeynikov <anton at korobeynikov.info>wrote: > > In the good old llvmc, the -Wo flag could be used to pass arguments to > the > > optimizer. Is there a similar mechanism anywhere for clang?

The llvm compiler can now generated movt/movw instructions to create 32-bit constants. Those new instructions use new relocations. Mach-o uses different numbering for relocations than ELF does. For mach-o, ARM_RELOC_PAIR=1 and ARM_RELOC_HALF=8. You need a newer linker that understands the new relocations. -Nick On Feb 20, 2012, at 5:20 AM, Harel Cain wrote: > Hi all, > > I'm

Hi all, I'm trying to figure out a problem with relocation types 1 and 8 (as observed using otool -r on ARM/Thumb object files). Earlier, when I used LLVM 2.8 with llc to generate thumb (-march=thumb -mattr=+thumb2) assembly listings, then assemble those using the gcc of iPhone 4.2 SDK, there wasn't any problem. However starting with LLVM 2.9, the same toolchain emits slightly different

How can I tell if this is normal behaviour? Oracle imports are horribly slow, an order of magnitude slower than on the same hardware with a slower disk array and Solaris 9. What I can look for to see where the problem lies? The server is 99% idle right now, with one database running. Each sample is about 5 seconds. I''ve tried setting kernel parameters despite the docs saying that

Hi I'm working on a POC adding Windows Phone (ARM) support to the ARM backend. I've encountered the following problem. Microsoft's COFF linker/loader supports a single relocation type ( IMAGE_REL_ARM_MOV32T) on continuous movw/movt Thumb2 instructions opposed to ELF and Mach-O which support relocation per instruction (one for movw and movt). I need to make sure that in case of

Hi When I'm using clang 3.1 with the isysroot argument, it doesn't seem to pick up header files from the directory I'm passing through the command line: > $ clang -isysroot/myownheaders -v foo.c -c -o foo.o > clang version 3.1 (tags/RELEASE_31/final) > Target: i386-pc-linux-gnu > Thread model: posix > "/usr/bin/clang" -cc1 -triple i386-pc-linux-gnu -emit-obj