Saving file after analysis in MeV

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Stacey
2010-06-22
2013-05-20
  • Stacey
    Stacey
    2010-06-22

    I am unable to save my .anl file after I do a SAM analysis.  The file says "saving" but then it just hangs there, for hours if I let it.  I have used this software before and have this happen on occasion, but now it happens every time.  I have used the software version from before Dec. 2009 and the newer one.  Both seem to give me this problem.

    Thanks for any advice.

    Stacey

     
  • Eleanor Howe
    Eleanor Howe
    2010-06-22

    Hi Stacey,

    I'm guessing that MeV is running out of memory while trying to save. Is your dataset large? Have you tried increasing the amount of memory allocated to MeV?

    From the FAQ at http://www.tm4.org/mev/?q=faq

    Q. How do I fix this Java.lang.outofmemory error?

    A. Sometimes huge data sets can cause out of memory errors. For some algorithms (notably HCL), we get out of memory errors if the number of genes is larger than about 10,000.

    If you are using a PC or a Linux machine, you can edit the TMEV.bat file (the file that you double-click on to start MeV) in a text editor and change the memory allocation. To this, find the text "java -Xmx512m" in the file, and replace 512 with 768 or 1024.

    Do any of these ideas help?
    Eleanor

     
  • Stacey
    Stacey
    2010-07-01

    Thanks for the info. I am using in with Mac OSX, Leopard.   I have 2GB of  RAM and about 14GB of free storage.  I am not sure what is considered a large data set.  I am mostly doing SAM analysis of Affymetrix based arrays.  Suggestions as to what is too big?  I also have had the same problem doing the analysis on a lab Dell with a bit more RAM and much larger hard drive.

    Thanks again,

    Stacey