Frequently Asked Questions

General Questions

  1. What are the pre-requisites for SAM?

    SAM 2.0 requires

    SAM version 1.21 and earlier required the Microsoft Java VM but current versions have eschewed Microsoft Java.

  2. How is SAM licensed? Whom should I contact?

    SAM is distributed without cost to Academic Institutions for research purposes. Academic users of SAM should cite the article below.

          @Article{TTC01,
          author = 	 {Tusher, V. and  Tibshirani, R. and Chu, C},
          title = 	 {Significance analysis of microarrays applied to
                      ionizing radiation response},
          volume = {98},
          year = {2001},
          journal = {Proceedings of the National Academy of Sciences},
          pages = {5116-5121},
          }
          

    They can download the software after registration directly from http://www-stat.stanford.edu/~tibs/SAM.

    Commercial users of SAM can download a limited version of SAM after registration from http://www-stat.stanford.edu/~tibs/SAM. For the complete version, please proceed to the SAM resource at the Stanford Office of Technology and Licensing.

  3. Is there a version of SAM that works on Macs?

    Unfortunately no. Since the Excel version of SAM makes extensive use of Microsoft component architecture on Windows, it is not easy to port it to Macs. You might get lucky try Virtual PC that comes with Microsoft Office Professional on Macs.

  4. Can I have access to the Web version of SAM?

    The Web version of SAM is no longer in development and is therefore not available anymore.

Registration Questions

  1. I registered for SAM and I have still not received an email confirming my registration.

    This is most likely due to your email server being down. Hundreds of requests have been successfully sent out to people. Our registration server tries every hour to remail the pending requests.

    If you do not receive your registration userid and password within the day, you may always register again and use another email address that works.

Installation, Uninstallation Questions

  1. When I try to install SAM, it complains that I need to install R version 2.0.x and above even when I have already done so!

    We have noticed this problem with situations where people have installed multiple versions of R. We suggest uninstalling all versions of R and reinstalling the latest version. While installing R make sure that you check the box to register the R path for use by the R DCOM server.

  2. How do I uninstall SAM?

    To uninstall, just use the Uninstall Menu. Or use the control panel to uninstall as you would any other program.

  3. How do I install a newly released version of SAM? Do I just install it on top of the old version?

    Installing new software on top of old versions is a good way to hose your Windows machine. If you want to preserve the little sanity that Windows has, you must first uninstall the old version and then install the new version.

  4. I upgrade my R installation and now SAM is not working!

    If you upgrade R, you need to uninstall and reinstall SAM. This is because SAM installs some R packages during the installation process, and these get installed in locations determined by the R version in effect.

    For those of you who are more adventurous/knowledgeable, essentially, one only need install the samr and impute packages from CRAN. Beware, however, of version dependencies; you are on your own here.

  5. I just downloaded your SAM program from your website and am having difficulty installing it. When I try to run the setup.exe it says it says something about not finding a folder!

    This is most likely due to the peculiarities of your computer.

    First make sure that your computer has sufficient disk space. It's an easy thing to forget, especially with the amount of crud that Internet Explorer keeps piling up in temporary folders.

  6. Where can I go for help if I just cannot get SAM to work?

    We are very interested in making SAM work for all users. However, before reporting problems or bugs, we'd really like you to make sure that the problem is really with SAM. The following checklist should help.

    If all this fails, then send email to sam-bug@stat.stanford.edu with complete details including

  7. Where is the SAM manual?

    It should be located in C:\Program Files\SAMVB\doc in the default installation. If you used a different directory, then it should be in the analagous place.

    In the worst case, search for the file sam.pdf.

  8. Where are the examples?

    They should be located in the C:\Program Files\SAMVB\Examples in the default installation. If you used a different directory, then it should be in the analagous place.

    In the worst case, search for the file twoclass.xls.

SAM Usage Questions

  1. SAM generates an error when I run it on my dataset. What should I do?

    Most often, errors are due to improper data formats.

    Sometimes SAM will run out of memory, especially if the dataset is large. The memory demands during the imputation phase coupled with other demands during the SAM phase can cause SAM to bomb. In such cases, typically, the imputation goes through. One can save the workbook, exit Excel and then rerun SAM on the imputed data.

  2. I get a message ``Excel is waiting for an OLE action to complete'' when I run SAM on my dataset? How can I stop this?

    At this point, we know of no way to stop this. There is a default time after which Excel will complain when a task takes too long. Moving to a faster computer usually helps.

    We hope to have a solution to this issue as soon as possible.

  3. Why does the random number seed stay the same? Can you not generate a new seed automatically?

    The random number seed allows one to reproduce an analysis. By default, it is set to 1234567. However, if one uses the default seed for every analysis, then the same sequence of permutations are generated. This is not always desirable. It would appear that generating a seed randomly using the clock or some such mechanism without bothering the user for input might be better. Not necessarily. If reproducibility is important, then asking the user to set the seed is preferable so that any analysis can be rerun to confirm results. We have come down on the side of reproducibility. The user always has a choice of requesting a randomly generated seed based on the clock by clicking on the Generate Random Seed button. Please also note that the random number generator seed used in any analysis is always listed in the output to ensure reproducibility of results.

  4. How large a dataset can SAM handle?

    There is really no hard limit per se in SAM. Excel itself has some limit on the number of rows and columns it can handle. R has some default limits on memory usage. (Future versions will allow facilities for configuring R). There are additional overheads involved in marshalling the data between Excel and the core of SAM. Therefore, the practical limit is lower. In general, the more memory you have, the larger problems you can handle. But at this point, the limit is the 32-bit implementation.

Trouble Shooting SAM

  1. How can I check if SAM installed properly?

    You should first check if the statconn DCOM server installed properly. Do this by choosing Start -> Programs -> statconn -> Basic server test. Test the 32-bit version.

    Next, you can fire up an R window, and just type

    library('samr')
    library('GSA')
    
    and ensure both load without error.

    Next check that the R DCOM server works. Choose Start -> statconn -> Basic server test and check that the 32-bit server test works.

    These three steps are generally sufficient.

  2. When I start Microsoft Excel, I get a Compile Error in Hidden Module! and SAM does not load.
  3. This seems to happen every time Windows updates Office components. The latest updates (Aug 2012) seem to unregister Microsoft's own DLLs (go figure!). Specifically, the DLL MSCOMCTL.OCX gets unregistered or somehow becomes unavailable. So one has to rectify this manually.

    Microsoft provides manual fixes for each of the cases below.

    If the above is too complicated for you, AT YOUR OWN RISK you can try downloading this file or save its contents as a .bat file. Then in a command window with administrative privileges (on windows 7, search for "cmd" and right-click to run as administrator) run this file.
    Last modified: Mon Jul 18 14:08:47 PDT 2001