Question

memory to use affy package

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Stephen Henderson ★ 1.0k

@stephen-henderson-71

Last seen 7.0 years ago

This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C255B8.FC98A200 Content-Type: text/plain I have been trying to use the affy package. I am running the Win32 version but I am finding that calculating expression values (HG133A X 6) crashes R. that is I run out of memory. e.g > express(Data,normalize=T, normalize.method="quantiles") Normalizing Data Background correcting Preparing Data Error: cannot allocate vector of size 32768 Kb In addition: Warning message: Reached total allocation of 500Mb: see help(memory.size) I have allocated the maximum for this computer e.g. > memory.limit(whatever) I have 3 questions that I would be grateful if anyone could help me with:- 1. Do all expression calculation and normalisation methods use similar amounts of memory (e.g loess?)? 2. Does the memory requirement for some methods rise as the chip numbers rise? 3. Reasonably how much memory do I need on a WIN32 to analyse HG133A chips? Many Thanks Stephen Henderson ********************************************************************** This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager (rmgztem@ucl.ac.uk). All files are scanned for viruses. ********************************************************************** ------_=_NextPart_001_01C255B8.FC98A200 Content-Type: text/html Content-Transfer-Encoding: quoted-printable <html> <head> <meta http-equiv="3D"Content-Type"" content="3D"text/html;" charset="3Dus-" ascii"=""> <meta name="3D"Generator"" content="3D"MS" exchange="" server="" version="" 5.5.2653.12"=""> <title>memory to use affy package</title> </head> <body>

I have been trying to u= se the affy package. I am running the Win32 version but I am finding that c= alculating expression values (HG= 133A X 6) crashes R. = that is I run out of memory.</fo=>

e.g

> express(Data,no= rmalize=3DT, normalize.method=3D"quantiles")

Normalizing Data</fo=>

Background correctin= g

Preparing Data</font=>

Error: cannot alloca= te vector of size 32768 Kb

In addition: Warning= message: 

Reached total alloca= tion of 500Mb: see help(memory.size)

I have allocated the ma= ximum for this computer

e.g.

> memory.limit(whatever= )

I have 3 que= stions that I would be gr= ateful if anyone could help me with:-

1. Do all expression ca= lculation and normalisation methods use similar amounts of memo= ry (e.g loess?)?

2. Does the memory requ= irement for some methods = rise as the chip numbers ris= e?

3. Reasonably h<= FONT SIZE=3D2 FACE=3D"Courier New">ow much memory do I need on a WIN32 to analyse HG133A chips?

Many Thanks

Stephen Henderson</font=>

<font size="3D3">



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affy affy • 985 views

ADD COMMENT • link 21.7 years ago Stephen Henderson ★ 1.0k

score 0 · Answer 1 · 2002-09-06

did you increase the memory allocated to R. with 6 chips, 256M should be enough -rafael On Fri, 6 Sep 2002, Stephen Henderson wrote: > I have been trying to use the affy package. I am running the Win32 version > but I am finding that calculating expression values (HG133A X 6) crashes R. > that is I run out of memory. > > e.g > > express(Data,normalize=T, normalize.method="quantiles") > Normalizing Data > Background correcting > Preparing Data > Error: cannot allocate vector of size 32768 Kb > In addition: Warning message: > Reached total allocation of 500Mb: see help(memory.size) > > I have allocated the maximum for this computer > > e.g. > > memory.limit(whatever) > > I have 3 questions that I would be grateful if anyone could help me with:- > > 1. Do all expression calculation and normalisation methods use similar > amounts of memory (e.g loess?)? > > 2. Does the memory requirement for some methods rise as the chip numbers > rise? > > 3. Reasonably how much memory do I need on a WIN32 to analyse HG133A chips? > > Many Thanks > Stephen Henderson > > > > ********************************************************************** > This email and any files transmitted with it are confidential and > intended solely for the use of the individual or entity to whom they > are addressed. If you have received this email in error please notify > the system manager (rmgztem@ucl.ac.uk). All files are scanned for viruses. > ********************************************************************** > >

score 0 · Answer 2 · 2002-09-06

On Fri, Sep 06, 2002 at 04:20:52PM +0100, Stephen Henderson wrote: > I have been trying to use the affy package. I am running the Win32 version > but I am finding that calculating expression values (HG133A X 6) crashes R. > that is I run out of memory. > > e.g > > express(Data,normalize=T, normalize.method="quantiles") > Normalizing Data > Background correcting > Preparing Data > Error: cannot allocate vector of size 32768 Kb > In addition: Warning message: > Reached total allocation of 500Mb: see help(memory.size) > > I have allocated the maximum for this computer > > e.g. > > memory.limit(whatever) > > I have 3 questions that I would be grateful if anyone could help me with:- > > 1. Do all expression calculation and normalisation methods use similar > amounts of memory (e.g loess?)? No. > > 2. Does the memory requirement for some methods rise as the chip numbers > rise? Yes. (for all methods) > > 3. Reasonably how much memory do I need on a WIN32 to analyse HG133A chips? > It depends on the number of chips. I am not very knowledgeable about the behavior of R and the package under Windows. Could you tell more about the number of chips you have loaded and the total amount of RAM your computer has ? > Many Thanks > Stephen Henderson > > > > ********************************************************************** > This email and any files transmitted with it are confidential and > intended solely for the use of the individual or entity to whom they > are addressed. If you have received this email in error please notify > the system manager (rmgztem@ucl.ac.uk). All files are scanned for viruses. > ********************************************************************** > -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent

score 0 · Answer 3 · 2002-09-07

My computer has 384Mb I'm told 256 should be sufficient (if slow). I think I have a problem with the memory allocation of my computer to R or my understanding of said process. I'll try reloading R--and see what happens. -----Original Message----- From: Laurent Gautier [mailto:laurent@cbs.dtu.dk] Sent: Friday, September 06, 2002 6:29 PM To: Stephen Henderson Cc: 'bioconductor@stat.math.ethz.ch' Subject: Re: [BioC] memory to use affy package On Fri, Sep 06, 2002 at 04:20:52PM +0100, Stephen Henderson wrote: > I have been trying to use the affy package. I am running the Win32 version > but I am finding that calculating expression values (HG133A X 6) crashes R. > that is I run out of memory. > > e.g > > express(Data,normalize=T, normalize.method="quantiles") > Normalizing Data > Background correcting > Preparing Data > Error: cannot allocate vector of size 32768 Kb > In addition: Warning message: > Reached total allocation of 500Mb: see help(memory.size) > > I have allocated the maximum for this computer > > e.g. > > memory.limit(whatever) > > I have 3 questions that I would be grateful if anyone could help me with:- > > 1. Do all expression calculation and normalisation methods use similar > amounts of memory (e.g loess?)? No. > > 2. Does the memory requirement for some methods rise as the chip numbers > rise? Yes. (for all methods) > > 3. Reasonably how much memory do I need on a WIN32 to analyse HG133A chips? > It depends on the number of chips. I am not very knowledgeable about the behavior of R and the package under Windows. Could you tell more about the number of chips you have loaded and the total amount of RAM your computer has ? > Many Thanks > Stephen Henderson > > > > ********************************************************************** > This email and any files transmitted with it are confidential and > intended solely for the use of the individual or entity to whom they > are addressed. If you have received this email in error please notify > the system manager (rmgztem@ucl.ac.uk). All files are scanned for viruses. > ********************************************************************** > -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent