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Contents

  1. Accounts
    1. Stanford Microarray Database(SMD) Accounts
      1. How do I acquire a SMD account?
      2. I've forgotten my SMD username and password?
      3. I can't open my SMD account
    2. FTP account on loader.stanford.edu
      1. Why would I need an ftp loader account?
      2. How do I acquire an ftp loader account?
      3. I've forgotten my loader account username and password?
      4. I can't find files on loader
      5. Freeing up space in your account
  2. Data entry
    1. How do I enter an experiment?
      1. How do I get started?
      2. Why don't my experiments have images?
      3. How is data normalization accomplished?
    2. How do I enter a new print?
    3. How do I initiate the process of entering a new organism in the database?
  3. Data Retrieval and Analysis
    1. Data Retrieval
      1. How do I find the data for a publication?
      2. How do I retrieve all the experiments for a print?
    2. Data Analysis
      1. Clustering : how do I get biological information included with my clusters?
      2. What do the asterisks mean in front of a Gene Name?
  4. Data and Database questions
    1. Data Questions
      1. What do these column names mean?
      2. Why are some experiments lacking data for the various median results?
      3. Which part of the array is used for determining background?
    2. Database questions
      1. What hardware and software does SMD run on?
      2. Can I set up a local version of SMD at my institution?

  1. Accounts

    1. Stanford Microarray Database(SMD) Accounts

      1. How do I acquire a SMD Account?

        The Stanford Microarray Database accounts are given to only:

        The SMD account application form, if you are one of the above, is here.

      2. I've forgotten my SMD username and password, and now I can't get in. Could you check on this for me?

        The curators do not know your password, so we can't remind you. They can, however, give you a new one which you may then change to one of your liking; just contact them.

      3. I can't log into SMD?

        • Make sure that the Caps Lock key is not depressed. Login names are not case sensitive, but passwords are.

        • Make sure your browser is set to accept cookies. It's usually in the "Advanced" subcategory under the "Preferences" menu in both IE and Netscape.

    2. FTP account on "loader.stanford.edu"

      1. Why would I need an FTP loader account?

        In order to load experiments into the database, the data-files themselves need to be located on our filesystem so that our software can parse and load them. In addition, the arraylists, genelists and ORA-OUT directory add additional functionality to your SMD account. Note: only unrestricted SMD users who are both performing array hybridizations and currently located at Stanford University can acquire an account.

      2. How do I acquire an FTP loader account?

        Ask an SMD curator at:array@genome.stanford.edu.

      3. I've forgotten my loader account username and password?

        The loader and SMD account usernames are the same. If you previously had a genome account, then the password to loader should be the same as your genome account. If your loader account was created at the same time as your SMD account, then their passwords should be the same, if you have not changed your SMD password. If you forgot these, the microarray curators can help you. Just email them at array@genome.stanford.edu.

      4. Can't Find Files on loader 
        	  > I am trying to batch submit files and cannot find the sample batch
	  > files. Can you please point me in the right
	  > direction?

        If you are using FTP Explorer, the best way to get to a new directory is to go under the Tools menu and select "Go To." You need to enter the full pathname of the file you want.

        If you are using Unix, type "cd " and the full pathname of the file.

      5. Freeing up space in your account 
        	  >What should I do if I don't have enough space in my directory?

        If you don't have enough space in your directory, you need to delete some files. The following commands may help you.

        • get filename copies a file from your current directory on loader in the directory from which you connected to loader. The file is not removed from your current directory.
        • delete filename removes the specified file from your current directory on loader. Once a file has been removed, that copy can no longer be accessed. Make sure you no longer need this file or have copied it elsewhere before using the delete command. FTP will not ask you to confirm this command before completing it.

        You can also save space by depositing compressed files.

  2. Data entry
    1. How do I load experiments?
      1. How do I get started?

        Entering an experiment requires that you have the files in your "loader.stanford.edu" account, in the "incoming" directory , so you will need an account on this system (a FTP loader account) to enter data. If you've never logged on to loader before, you may not have an account on loader. Keep in mind that a loader account is different from a SMD Database access account. Please refer to the SMD Account and Access help page for additional information on SMD accounts, viewing data, and entering experiments.

      2. Why don't my experiments have images?

        With some experiments, the software program that makes the images(.gif files) fails when the experiments are entered into the database, so these experiments will not have any images in the database.

      3. How is data normalization accomplished? 
        	  >How do I do normalization?

    2. How do I enter a new print?

      1. First you need to create a godlist containing essential information about your samples. The godlist help file explains what information you need to collect.
      2. After depositing the godlist in your ORA-OUT folder on loader.stanford.edu, you can validate the godlist using the following program.
      3. If your samples require the assigment of new SUIDs, e-mail the curators at SMD (array@genome.stanford.edu) and they will assign the new SUIDs.
      4. After validating the godlist you will receive a message telling you what additional information you need to e-mail the curators (array@genome.stanford.edu) about the printing. They will create the printlist for you.

    3. How do I initiate the process of entering a new organism in the database?
      Please send an e-mail to the curators at array@genome.stanford.edu.

  3. Data Retrieval and Analysis

    1. Data Retrieval

      1. How do I find the data for a publication?
        To download data from a publication follow the Published data link on the SMD homepage. The "SMD" link in the last column will take you to the page where you can download the complete set of data in a compressed format ("raw data"). You can also display or analyze the arrays by choosing the appropriate buttons at the bottom.

        You can also do this by selecting "publications", organism and reference in the basic search window. The "display data" button will take you to the window where you download the data.

        The Retrieving Public Data from SMD help will give you more detailed information on this topic.

      2. How do I retrieve all the experiments for a print?
        Database users can retrieve data from a print by using "method 2" and selecting the desired print name on the Advanced Results Search page.

    2. Data Analysis

      1. Clustering and Biological Annotations 
        	  >how do I have gene names or other biological information show up on my clusters?

        After selecting the experiments you wish to cluster, you are presented with a page of clustering options. These include "Gene Selection Options", "Gene Filtering", "Biological data To Select", and "Data Selection Options". Within the third field, "Biological data To Select", you can choose which annotations to display alongside your cluster. For example, for yeast you may display the gene name, process, and function. The default clustering display does not include biological annotations, only the systematic name. Also, biological information contained within SMD varies depending on the level of annotation for your organism of interest.

      2. What do the asterisks mean in front of a Gene Name?

        The asterisks are there to warn users. There are a number of clones that map to more than one UniGene clusters. These clones are often referred to as "chimeric clones" because their 5' and 3' ends are most likely derived from different messages. We flag these clones with double asterisks under their GENE_NAME annotation to signify that we are choosing one of the possible annotations. Users should take caution in interpreting their results from these clones (and not take them *too* seriously), and perhaps study them more closely.

  4. Data and Database questions

    1. Data Questions

      1. What do these SMD data abbreviations (column names) mean? 
        	  >How can I find out what the SMD column names mean?
	  >For example, what is the LFRAT column?
        Explanations of the column names can be found in the ScanAlyze manual in the MicroArray software section.

        Other information is available from the database table specifications section; data columns are described in the results table.

      2. Why are some experiments lacking data for the various median results?

        Data entered before January 2001 does not contain these median result data. Before this time, our default file format was based on Scanalyze, which does not have these columns. Since the beginning of 2001, we changed our database so that it was able to store all columns produced by Genepix, which is used by most people entering data into SMD, while continuing to support Scanalyze.

      3. Which part of the array is used for determining background?

        Background is determined on a local, spot-by-spot basis. If you are using Genepix, the background pixels include all of the pixels within a circular region that surround the feature of interest unless they meet one of the conditions listed below. The circular region has a diameter of three times the diameter of the current feature indicator. The pixel is excluded from background calculation if one of the following is true:
        1) the pixel resides in a neighboring feature-indicator
        2) the pixel is not wholly outside a two pixel wide ring around a feature-indicator
        3) the pixel is within the feature-indicator of interest.

    2. Database questions

      1. What hardware and software does SMD run on?

        Information on the hardware and software used by SMD is available on SMD's About page

      2. Can I set up a local version of SMD at my institution?

        Absolutely, in fact we strongly encourage it! All of SMD's software is available for download here, and there is a development forum for people to ask questions or post suggestions about SMD's code. We hope the net result will be that SMD will improve.

Please send comments or questions to: array@genome.stanford.edu