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SAM - time course analysis

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Stefan
2010-09-01
2013-05-20
  • Stefan
    Stefan
    2010-09-01

    Hello,
    I tried to conduct a time course analysis (2 conditions, 4 time points, condition 1: 10 replicates, condition 2: 4 replicates) with the SAM module in version 4.6.1 and have some questions:

    1) What does the column with the "0.0" values stand for? Is it a tool for the assignment of the different time points? If yes, do I have to click the "Start" and "End" buttons in addition? I could not find a description of these new features in the manual.

    2) I tried to save the grouping but only Condition 1 and 2 are kept, my input for "0.0", "End", and "Start" is always lost.

    3) Do I have to enable the "Use R" option? It is possible to conduct the analysis by clicking the "Time Course Data" Button without activating the "Use R" option, but the result seems to be quite meaningless.

    4) When I activate the "Use R" option, the following error occurs:

    user.home C:\Dokumente und Einstellungen\stefant
    user.dir C:\software\MeV_4_6_1
    Checking for R_HOME : C:\software\MeV_4_6_1\R-2.9.1
    Could not retreive Web Repository Info.
    sun.net.ftp.FtpProtocolException: PORT :501 PORT not allowed after EPSV ALL

            at sun.net.ftp.FtpClient.openDataConnection(Unknown Source)
            at sun.net.ftp.FtpClient.get(Unknown Source)
            at sun.net.www.protocol.ftp.FtpURLConnection.getInputStream(Unknown Source)
            at org.tigr.rhook.RHook.getPropInfoRhook(RHook.java:1009)
            at org.tigr.rhook.RHook.loadRHookProperties(RHook.java:218)
            at org.tigr.rhook.RHook.startRSession(RHook.java:159)
            at org.tigr.microarray.mev.cluster.algorithm.impl.SAM.runRAlg(SAM.java:1187)
            at org.tigr.microarray.mev.cluster.algorithm.impl.SAM.execute(SAM.java:799)
            at org.tigr.microarray.mev.cluster.gui.impl.sam.SAMGUI.execute(SAMGUI.java:468)
            at org.tigr.microarray.mev.MultipleArrayViewer$7.run(MultipleArrayViewer.java:2615)
            at java.lang.Thread.run(Unknown Source)
    Error loading R

    Maybe, this is a problem with our proxy server. Do you have an idea how to solve it?

    Thank you very much in advance for your help!

    STefan

     
  • Hi Stefan,

    1) You are correct, it is for assigning different time points and you must still select start and end for each time course.
    2) Thanks for the bug report, we will address this in our next release.
    3) Yes, the time course analysis uses R, so "use R" is necessary.
    4) Thanks for the report, we are looking into the problem.

    Dan

     
  • Stefan
    Stefan
    2010-09-03

    Hi Dan,
    Thanks for your kind help.
    @4) I tried to run the R-dependent modules on my home computer and they worked quite well. It seems to be a problem with the firewall or the proxy server in my company.
    Nevertheless, I got a different error message for SAM. But maybe this is caused by a lack of memory, I´ll figure it out.

    Stefan