From khansen at stat.Berkeley.EDU  Sun Dec 18 03:52:12 2005
From: khansen at stat.Berkeley.EDU (Kasper Daniel Hansen)
Date: Sat, 17 Dec 2005 18:52:12 -0800
Subject: [Rd] R for Windows GUI Front-End Problem (PR#3364)
In-Reply-To: <43A1D553.8060600@usc.edu>
References: <43A1D553.8060600@usc.edu>
Message-ID: <FDE1C963-6178-4F3F-B1A1-FADD8A8EB5DF@stat.berkeley.edu>

Please use the BioC list for questions such as this. It has been  
discussed numerous times there. I am cc: my answer to that list.

On Dec 15, 2005, at 12:42 PM, Pathik wrote:

> Dear Programmers,
>
>     I encounter following error,while loading vector.
>
>> pam_Test<- ReadAffy()
> Error: cannot allocate vector of size 312879 Kb
> In addition: Warning messages:
> 1: Reached total allocation of 1024Mb: see help(memory.size)
> 2: Reached total allocation of 1024Mb: see help( memory.size)

This just means you do not have enough memory. Do not fret over the  
specific values, R just bangs out at some kind of assignment  
somewhere in the code.

> I also changed headers to use maximum memory as i am having 4GB of
> physical memory in my machine.but still i am facing problem.

Well, you still do not have enough ram. Note though that R cannot use  
all of the 4GB due to limitations of the OS. So it will not help to  
add more RAM.

> Is ther any other soution?

Install an OS which can actually use all your RAM.

You could try reading in smaller subsets of the data, instead of  
everything in one go, although you will probably have problems when  
you normalize (at least if you want to normalize all chips together).  
How many chips are you looking at (and how big are they?)

Kasper

> -- 
> Pathik Patel
> Graduate Student,
> Ph-213-321-1360
> ====================================================================== 
> =
> UNIX is an operating system, OS/2 is half an operating system,  
> Windows is a shell, and DOS is a boot partition virus
>
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> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] R for Windows GUI Front-End Problem (PR#3364)
Kasper Daniel Hansen