[BioC] memory to use affy package

Fri, 6 Sep 2002 16:20:52 +0100

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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

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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=
NT>

<P ALIGN=3DLEFT><FONT SIZE=3D2 FACE=3D"Courier New">e.g</FONT></P>

<P ALIGN=3DLEFT><I><FONT SIZE=3D2 FACE=3D"Courier New">&gt; express(Data,no=
rmalize=3DT, normalize.method=3D&quot;quantiles&quot;)</FONT></I></P>

<P ALIGN=3DLEFT><I><FONT SIZE=3D2 FACE=3D"Courier New">Normalizing Data</FO=
NT></I></P>

<P ALIGN=3DLEFT><I><FONT SIZE=3D2 FACE=3D"Courier New">Background correctin=
g</FONT></I></P>

<P ALIGN=3DLEFT><I><FONT SIZE=3D2 FACE=3D"Courier New">Preparing Data</FONT=
></I></P>

<P ALIGN=3DLEFT><I><FONT SIZE=3D2 FACE=3D"Courier New">Error: cannot alloca=
te vector of size 32768 Kb</FONT></I></P>

<P ALIGN=3DLEFT><I><FONT SIZE=3D2 FACE=3D"Courier New">In addition: Warning=
 message: </FONT></I></P>

<P ALIGN=3DLEFT><I><FONT SIZE=3D2 FACE=3D"Courier New">Reached total alloca=
tion of 500Mb: see help(memory.size)</FONT></I><I></I></P>

<P ALIGN=3DLEFT><FONT SIZE=3D2 FACE=3D"Courier New">I have allocated the ma=
ximum for this computer </FONT></P>

<P ALIGN=3DLEFT><FONT SIZE=3D2 FACE=3D"Courier New">e.g.</FONT></P>

<P ALIGN=3DLEFT><FONT SIZE=3D2 FACE=3D"Courier New">&gt;</FONT><I> <FONT SI=
ZE=3D2 FACE=3D"Courier New">memory.limit(</FONT></I><I><FONT SIZE=3D2 FACE=
=3D"Courier New">whatever</FONT></I><I><FONT SIZE=3D2 FACE=3D"Courier New">=
)</FONT></I></P>

<P ALIGN=3DLEFT><FONT SIZE=3D2 FACE=3D"Courier New">I have</FONT> <FONT SIZ=
E=3D2 FACE=3D"Courier New">3</FONT><FONT SIZE=3D2 FACE=3D"Courier New"> que=
stions</FONT><FONT SIZE=3D2 FACE=3D"Courier New"> that I would be gr</FONT>=
<FONT SIZE=3D2 FACE=3D"Courier New">a</FONT><FONT SIZE=3D2 FACE=3D"Courier =
New">teful if anyone could help me with</FONT><FONT SIZE=3D2 FACE=3D"Courie=
r New">:-</FONT></P>

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?

<P ALIGN=3DLEFT><FONT SIZE=3D2 FACE=3D"Courier New">Many Thanks</FONT></P>

<P ALIGN=3DLEFT><FONT SIZE=3D2 FACE=3D"Courier New">Stephen Henderson</FONT=
></P>

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