[BioC] Regarding error while normalizing using "loess" method

[James W. MacDonald]

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 at 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 at 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


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Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.