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

[James W. MacDonald]

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]]
> 
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-- 
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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