Displaying 4 results from an estimated 4 matches for "liwong".
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lirong
2005 Jan 03
2
Memory problem ... Again
...P3a
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 305954055 2334.3
...
> mem.limits(...
2007 Dec 24
3
Affy Package
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, ARS
National Center for Cool & Cold W...
2004 Dec 28
2
Configuration of memory usage
...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 305954068 2334.3
> object.size(Dat...
2005 Jul 19
1
mac os x crashes with bioconductor microarray code (PR#8013)
...ULL) (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 szone_error to debug
R(1763) malloc: **...