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Question: Affy. memory allocation trouble!
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gravatar for Jens Vilstrup Johansen
16.0 years ago by
Jens Vilstrup Johansen20 wrote:
This is a multi-part message in MIME format. ------_=_NextPart_001_01C2913D.D3057CE0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi I get this error message. How do I solve this? >library(affy) > Data <- ReadAffy () reading CDF file processing information reading 2 CEL files.. preparing probe level object Error: cannot allocate vector of size 3874 Kb In addition: Warning message:=20 Reached total allocation of 127Mb: see help(memory.size)=20 I don't know if this is helpfull: > gc() used (Mb) gc trigger (Mb) Ncells 301800 8.1 1068187 28.6 Vcells 66248 0.6 8156627 62.3 > memory.size() [1] 102909640 > memory.limit() [1] 133619712 Thanks! regards, Jens Johansen ------_=_NextPart_001_01C2913D.D3057CE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable <html> <head> <meta http-equiv="3D"Content-Type"" content="3D"text/html;" =="" charset="3Diso-8859-1""> <meta name="3D"Generator"" content="3D"MS" exchange="" server="" version="6.0.5762.3""> <title>Affy. memory allocation trouble!</title> </head> <body>

<font size="3D2" face="3D"Courier" new"="">Hi</font>

<font size="3D2" face="3D"Courier" new"="">I get this error message. How do = I solve this?</font>

<font size="3D2" face="3D"Courier" new"="">>library(affy)</font>
<font size="3D2" face="3D"Courier" new"="">> Data <- ReadAffy = ()</font>
<font size="3D2" face="3D"Courier" new"="">reading CDF file</font>
<font size="3D2" face="3D"Courier" new"="">processing information</font>
<font size="3D2" face="3D"Courier" new"="">reading 2 CEL files..</font>
<font size="3D2" face="3D"Courier" new"="">preparing probe level = object</font>
<font size="3D2" face="3D"Courier" new"="">Error: cannot allocate vector of = size 3874 Kb</font>
<font size="3D2" face="3D"Courier" new"="">In addition: Warning message: = </font>
<font size="3D2" face="3D"Courier" new"="">Reached total allocation of = 127Mb: see help(memory.size) </font>

<font size="3D2" face="3D"Courier" new"="">I don't know if this is = helpfull:</font>
<font size="3D2" face="3D"Courier" new"="">> gc()</font>
<font size="3D2" face="3D"Courier" =="" new"="">         used (Mb) gc = trigger (Mb)</font>
<font size="3D2" face="3D"Courier" new"="">Ncells 301800  = 8.1    1068187 28.6</font>
<font size="3D2" face="3D"Courier" new"="">Vcells  66248  = 0.6    8156627 62.3</font>

<font size="3D2" face="3D"Courier" new"="">> memory.size()</font>
<font size="3D2" face="3D"Courier" new"="">[1] 102909640</font>

<font size="3D2" face="3D"Courier" new"="">> memory.limit()</font>
<font size="3D2" face="3D"Courier" new"="">[1] 133619712</font>

<font size="3D2" face="3D"Courier" new"="">Thanks!</font>
<font size="3D2" face="3D"Courier" new"="">regards,</font>
<font size="3D2" face="3D"Courier" new"=""> Jens Johansen</font>

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ADD COMMENTlink modified 16.0 years ago by rgentleman5.5k • written 16.0 years ago by Jens Vilstrup Johansen20
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gravatar for rgentleman
16.0 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
On Thu, Nov 21, 2002 at 10:10:23AM +0100, Jens Vilstrup Johansen wrote: > Hi > > I get this error message. How do I solve this? > > >library(affy) > > Data <- ReadAffy () > reading CDF file > processing information > reading 2 CEL files.. > preparing probe level object > Error: cannot allocate vector of size 3874 Kb > In addition: Warning message: > Reached total allocation of 127Mb: see help(memory.size) Hi, help(Memory) has some information. It could be a limit set (either by you or by the available resources). - if it doesn't then I suggest the R mail archive (searchable). It can be found off of www.r-project.org Robert > > I don't know if this is helpfull: > > gc() > used (Mb) gc trigger (Mb) > Ncells 301800 8.1 1068187 28.6 > Vcells 66248 0.6 8156627 62.3 > > > memory.size() > [1] 102909640 > > > memory.limit() > [1] 133619712 > > Thanks! > regards, > Jens Johansen > -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+
ADD COMMENTlink written 16.0 years ago by rgentleman5.5k
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