SMD : Help : Help Entering Results for a Single Array

Help : Help Entering Results for a Single Array

Contents

Description

The Data Entry for Microarray Experiment form is used to enter experiments into the database one at a time. This help describes how to fill out the form to enter an experiment. Experiments can also be entered by batch, and a separate batch help is available for that procedure.


It is assumed you've already read First Time Users and What You Need from the previous help file, Entering Results from Experiments

Completing the Data Entry for Microarray Experiment Form

Result Set Section (Affymetrix and Agilent only)

A "Result Set" is one version of the data for a given hybridization. The Agilent and Affymetrix/dChip software will allow you to set various parameters, producing somewhat different numbers. That is, you may scan a slide once (defining a "slide" and "experiment" for the purposes of the database), but choose several different ways to normalize or compute the extracted data, producing multiple result sets for the single slide. Additionally, the Affymetrix cell file is considered a separate result set for Affymetrix arrays (you should have exactly one cell file result set, and one or more data file result sets, per Affymetrix array).

  1. Enter the name for the result set and a description specific to the set; e.g., details of the normalization, or the software used (say, MAS 5 vs. GCOS vs. dChip). Information describing the experiment or encompassing all result sets (e.g., for Affymetrix, the cell data and every Probe Set intensity set) is entered in the Experiment Description and Details section.

Data File Locations Section

  1. Determine the print your experiment uses and select it from the pop-up list. Clicking on Print Name will get you information about these prints. If you are unsure about which print to use, contact the microarray database curators.

  2. Enter a unique name for the slide used in this experiment in the Slide Name box. A systematic slide name, usually dictated by the array producer, is preferred (unique).

    Note: All text entry on the forms is case sensitive. Also, please avoid the use of single and double quotes ('a' and "a") in your entries.

  3. Select the files from the pull-down menu containing data for your experiment. These files must exist in the Stanford Department of Genetics UNIX system. To transfer files from a PC to this system, ftp to loader.stanford.edu (you must already have an account on loader). After you have logged into your directory, go to your incoming directory and place your data files there. The incoming directory in your own account on loader is the only place from which you can load data. Please make sure that you transfer your .gpr, .dat, .srr, .CEL, .xls, and .txt files as ASCII text and the .gps, .sag, .sra, .tif, and Affymetrix .DAT files as binary or "raw" data. Remember that we now accept compressed (.gz) files. For more information about transferring files, refer to the Entering Results from Experiments document.

Experiment Description And Details Section

  1. Enter a date you want associated with the experiment; the date of hybridization is recommended. The date format is 4-digit year, 2-digit month, and 2-digit day (YYYY-MM-DD).

  2. For Experiment Name, enter a unique, descriptive name for your experiment. The maximum length is 100 characters.

  3. You have space to enter 2000 characters of text description for experiment. This is optional and is intended for useful notes, such as a description of the methods used in sample preparation. There are separate description fields below to specifically identify the red and green channels.

  4. Choose an experiment category and subcategory. If you need more information about categories or subcategories, click on the links to the left of the pop-up menus. If you need new categories or subcategories created, contact the microarray database curators.

  5. Enter short descriptions of the samples used for the green and red channels in this experiment. The maximum length is 100 characters, and descriptions are usually phrases such as "reference pool", or "nitrogen starvation, 2 days".

  6. If you wish to define your own normalization, check 'User Defined' and enter a normalization value in the box provided. Otherwise, accept the default-computed normalization ('Computed' on the form) or select 'Using regression correlation' if you wish to use this method. Normalization type is required for entering Agilent Affymetrix data, but is ignored.

Array Access Section

  1. Enter the login name of the person who performed the experiment in the Experimenter box. This will be the only person, save the curators, with the ability to edit or delete the array. By default, your entire lab group will automatically have view access to your experiment.

  2. Choose who will be able to see the data from your array using the multiple-select scrolling lists under Collaborative Group. You may select one or more Collaborative Groups and/or one or more individual users who will be able to view your data. (To select multiple choices in a list, hold down the command/apple key on MacOS or the control key on a Windows while you click. With Unix, just click on multiple names.) Lists of collaborative groups and individual users can be obtained by clicking the links to the left of the scrolling menus or by clicking "User group" or "Users" under "List Data" on the main page.

  3. Click the "Load Experiment into Database" button to enter your experiment.

Monitoring Your Request as it Progresses Within the Queue

Experiment loading is commenced by entering your loading-data into a queue. The rate of loading is determined by a number of factors, including both the load on the database and how many other array-load requests were made prior to yours. If there are no delays, it usually takes at least five minutes per array, and may take quite a bit longer if your arrays have a large number of spots (human arrays) or if many other users are using the database. During this time, you can check the progress of your experiment load within the queue. After your data is successfully entered into the queue (Note: this is not the same thing as final entry into the database), you should receive a confirmation screen as well as an email notifying you: 

	Your database entry request (batch number XXXX) has been
queued for loading.

	Please note the data for your array(s) ARE NOT YET IN THE
DATABASE.  Do NOT delete any of your files until you receive email
confirmation that the data have been loaded.

	Progress of is batch within the queue can be viewed at:

http://genome-www5.stanford.edu/cgi-bin/tools/queue/nph-ProgressQuery?batchno=XXXX

	You may also view this file in your loader account under the ORA-OUT directory.
	If you have any questions please contact the curators 

	array@genome.stanford.edu)

You can check the progress of your experiment load based on the batch number reported to you with either the link on the queue confirmation page or from the URL in the email.


Successful Result Entry into the Database

If all goes well, you will eventually get an email message that says:


        Loading of your array data (batch number XXXX), has
successfully completed. 1 out of 1 were successfully loaded.

	Details of the load process have been written to :
        
	/loader/ftphome/username/ORA-OUT/XXXX.log,

or you can temporarily view the details via the web at:

http://genome-www5.stanford.edu/cgi-bin/tools/queue/nph-ProgressQuery?batchno=XXXX

	If you have any questions please contact the curators

	(array@genome.stanford.edu).
At the bottom of the HTML confirmation page or in the log file in your ORA-OUT directory on loader.stanford.edu should be the message:
***All data for this experiment ('slidename') have been successfully inserted into oracle database***

Common Problems

  1. If your results have not been loaded 1 day after entry into the queue, please notify the microarray database curators.

  2. File location: All files must be in the incoming directory on your account for loader.stanford.edu.

  3. UNIX file names: The names of your uploaded files should not contain spaces, or any of the following characters:
    '  "  #  ,  /  \  ?  <  >  ;  :  !  @  %  ^  &  *  (  )

  4. Occasionally, we backup and re-index the database. This process can significantly the delay the loading of data (and vice versa). We suggest not loading during these time periods. Consult the Scheduled Database Backups page for the times to avoid.

  5. Sometimes .tif -> .gif conversion fails. Please check your loaded arrays by displaying them and verifying the clickable-gif. If you need to replace the gif file that we have created for you, please see our help documentation for this. If their is no clickable-gif icon present, contact the microarray database curators.

  6. Errors? What errors? Shortly after a queue batch request is processed (successful or not), you will no longer be able monitor its status within the queue (as it has been removed, and its web-log with it). However, just check your ORA-OUT directory on loader.stanford.edu to see the text log-file of the database entry.

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