SAM 2.0 requires
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.
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.
The Web version of SAM is no longer in development and is therefore not available anymore.
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.
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.
Please go to the microsoft office website and make sure that you have the latest updates to Microsoft Office. Click on Downloads to install the updates.
To uninstall, just use the Uninstall Menu. Or use the control panel to uninstall as you would any other program.
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.
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.
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.
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.
sam-bug@stat.stanford.edu with
complete details including
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.
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.
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.
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.
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.
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.