Hi Raghavendra,
20 samples is not so many. If you are still getting the 'out of memory' error,
please send me the project file that is causing the error so I can take a look
at it (use e.g. http://www.dropsend.com/).
Tomas
On Jul 4, 2012, at 9:03 PM, Raghavendra Gunnaiah wrote:
Dear Dr. Tomas,
4 hours is too long. But you forgot to write how many samples you load at once.
I load 20 samples at once (4 treatments X 5 replications). Is it possible to
run one treatment (5 samples) at a time and later combine all (like metaXCMS)?
Use more memory or optimize your parameters (noise level, m/z tolerance etc.)
to reduce the amount of noise peaks produced.
Max RAM in my computer is 4 gb and i have allocated 3 gb for mzmine. I will try
optimizing noise level and m/z tolerance. At present I am using noise level=
5000, and m/z tolerance=10 ppm (orbitrap with 60,000 mass resolution).
Thank you for the quick reply
with kind regards
Raghavendra Gunnaiah
Ph.D Scholar
R1-013,Department of Plant Science
McGill University Macdonald Campus
21,111 Lakeshore Road
Ste. Anne de Bellevue, QC H9X 3V9
________________________________
From: Tomas Pluskal [plus...@oist.jp<mailto:plus...@oist.jp>]
Sent: July 3, 2012 9:27 PM
To: Developer discussion
Cc: Raghavendra Gunnaiah
Subject: Re: [Mzmine-devel] project opening error
Hi Raghavendra,
My questions
1. Is this long time taking process normal? If not, what changes I have to make
in the log file
4 hours is too long. But you forgot to write how many samples you load at once.
2. How can I overcome the above error?
Use more memory or optimize your parameters (noise level, m/z tolerance etc.)
to reduce the amount of noise peaks produced.
3. I would like to use Wavelets (XCMS) for deconvolution. I have given correct
path to R (2.15.1) and have installed xcms 1.33.13 (the latest available
version in bioconductor). But the method asks for xcms version 1.33.2 or later.
Where can I find xcms 1.33.2
Chris might take a look at this..
Best regards,
Tomas
===============================================
Tomáš Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
TEL: +81-98-966-8684
Fax: +81-98-966-2890
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Tomáš Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
TEL: +81-98-966-8684
Fax: +81-98-966-2890
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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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