hi James,

I tried debugging. But , I cant make any thing out of it.

When shut and open the R environment , the loess is running. I dont know
even why it is running.. but happy.

And, I cannot really solve the memory problem. If I give the full dataset,
it says there is problem in creating vector. Here is the set of commands.

**************************************************************************
> memory.limit()
[1] 1063641088
> memory.limit(size = 4000)
NULL
> memory.limit()
[1] 4194304000
> ls()
[1] "cel.data" "exp.data"
> rm (list = ls())
> ls()
character(0)
> cel.data <- ReadAffy()
> memory.limit()
[1] 4194304000
> exp.data <- expresso(cel.data,bgcorrect.method="mas",normalize.method=
"loess",pmcorrect.method="mas",summary.method="medianpolish",verbose=TRUE)
background correction: mas
normalization: loess
PM/MM correction : mas
expression values: medianpolish
background correcting...Error: cannot allocate vector of size 201117 Kb
>
*************************************************************************

but the process ran overnight. I could not make out anything of it.
Presently, I am working in a windows system with 1GB RAM.

Thank you,
Ganiraju



On 10/3/06, James W. MacDonald <jmacdon@med.umich.edu> wrote:
>
> Ganiraju Manyam wrote:
> > hi James,
> > Thanks for the info.
> >
> > Here is the copy of console.
> >
> >
> ************************************************************************************
> >
> >
> >
> >> sessionInfo()
> >
> > Version 2.3.1 (2006-06-01)
> > i386-pc-mingw32
> >
> > attached base packages:
> > [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
> > [7] "datasets"  "base"
> >
> > other attached packages:
> > hgu133plus2cdf           affy         affyio        Biobase
> >      "1.12.0"       "1.10.0"        "1.0.0"       "1.10.1"
> >
> >> cel.data <- ReadAffy()
> >> exp.data <- expresso(cel.data,bgcorrect.method = "mas",
> >> normalize.method =
> >
> > "loess", pmcorrect.method = "mas", summary.method ="medianpolish")
> > background correction: mas
> > normalization: loess
> > PM/MM correction : mas
> > expression values: medianpolish
> > background correcting...done.
> > normalizing...Error in matrix(0, II, J) : non-numeric matrix extent
>
> That's odd. I can get this call to expresso() to work here with the same
> packages. What happens if you do this:
>
> debug(normalize.loess)
> cel.data <- ReadAffy()
> exp.data <- expresso(cel.data,bgcorrect.method = "mas", normalize.method
> = "loess", pmcorrect.method = "mas", summary.method ="medianpolish")
>
> Then when you enter the debugger, you type dim(mat) and then class(mat)?
>
> Best,
>
> Jim
>
>
>
> >> exp.data <- expresso(cel.data,bgcorrect.method = "mas",
> >> normalize.method =
> >
> > "quantiles", pmcorrect.method = "mas", summary.method ="medianpolish")
> > background correction: mas
> > normalization: quantiles
> > PM/MM correction : mas
> > expression values: medianpolish
> > background correcting...done.
> > normalizing...done.
> > 54675 ids to be processed
> > |                    |
> > |######
> > ##############|
> >
> >>
> >
> >
> ***********************************************************************************************
> >
> >
> > The problem occurs only will "loess" method and is working fine when i
> use
> > "quantiles" or "constant" normalization.
> >
> > Thank you,
> > Ganiraju
> >
> >
> > On 10/2/06, James W. MacDonald <jmacdon@med.umich.edu> wrote:
> >
> >>
> >> Hi Ganiraju,
> >>
> >> Ganiraju Manyam wrote:
> >> > hi all,
> >> >
> >> > I am Ganiraju, a new member of the group. (and currently using the
> affy
> >> > package)
> >> >
> >> > I m trying to use "loess" method in expresso function to normalize
> the
> >> data.
> >> >
> >> > While running Im getting an error: "non-numeric matrix extent"
> >> >
> >> > I didnt really understand whether is some problem with ReadAffy(), or
> >> > functinoality of "loess", whether it can be used on all kinds of
> >> data or
> >> > not.
> >>
> >> You really need to give more information than this. At a minimum, you
> >> need to give the commands you ran along with the results (i.e., copying
> >> and pasting from within R). You should also give the results that you
> >> get when you run sessionInfo() after loading all the packages you are
> >> using here.
> >>
> >>
> >> >
> >> > Also, Im runnig sort of memory. Is there any other way to create
> >> virtual
> >> > memory other than using "memory.limit."
> >>
> >> Assuming you are on windows, as AFAIK, this command doesn't exist for
> >> *nix or MacOS, the short answer is no. You can set the command line
> flag
> >> --max-mem-size in the shortcut you use to launch R, setting this value
> >> to the amount of RAM you have. If you still run out of memory, the next
> >> step is to buy more RAM. R on windows will usually stop a computation
> >> rather than using virtual memory (much to its credit IMO). Trying to do
> >> any real computation using virtual memory is too painfully slow to be
> >> recommended.
> >>
> >> Best,
> >>
> >> Jim
> >>
> >>
> >> >
> >> > Thanks in advance,
> >> > Ganiraju
> >> >
> >> >       [[alternative HTML version deleted]]
> >> >
> >> > _______________________________________________
> >> > Bioconductor mailing list
> >> > Bioconductor@stat.math.ethz.ch
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >> --
> >> James W. MacDonald, M.S.
> >> Biostatistician
> >> Affymetrix and cDNA Microarray Core
> >> University of Michigan Cancer Center
> >> 1500 E. Medical Center Drive
> >> 7410 CCGC
> >> Ann Arbor MI 48109
> >> 734-647-5623
> >>
> >>
> >> **********************************************************
> >> Electronic Mail is not secure, may not be read every day, and should
> not
> >> be used for urgent or sensitive issues.
> >>
> >
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not
> be used for urgent or sensitive issues.
>

	[[alternative HTML version deleted]]

