Displaying 5 results from an estimated 5 matches for "invariantset".
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invariants
2008 Mar 20
2
Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character"
...t.
My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains
the Microarray Expression Values collected from the Illumina Microarray
experiment. These collected intensity values need to be normalized(Rank
Invariant Normalization) by using the R function
"normalize.AffyBatch.invariantset()".
Since the normalize.AffyBatch.invariantset() method requires the input
argument to be an AffyBatch Object, I used the read.exprSet() method to
convert the intensity values present in the (textE_to_affy.csv) file into an
AffyBatch Object as follows:
> testFile <- tempfile()
>te...
2005 Jan 03
2
Memory problem ... Again
...Our system is like this:
System type: IBM AIX Symmetric Multiprocessing (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...
2004 Dec 28
2
Configuration of memory usage
...y(filenames = paste(HOME, "CelData/", fname, sep=""))
> 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...
2005 Jul 19
1
mac os x crashes with bioconductor microarray code (PR#8013)
Full_Name: Eric Libby
Version: 2.1.1
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 alloca...
2010 Aug 04
1
error with ReadAffy()
Hi!I'm doing a little data importing from .cel files,
> setwd("/home/mandova/celfiles")
> mydata<-ReadAffy()
Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) :
unused argument(s) (extended = TRUE)
Then I tried
> filenames<-paste("GSM",c(seq(138597,138617,1)),".cel",sep="")
>