Help : Repository Help
Contents
Related Help Documents
- Data
Selection for Analysis: Explanation of the steps involved in
selecting and filtering data for clustering
- Analysis
Methods: Information about the algorithms used for hierarchical
clustering and Self-Organizing Maps (SOMs)
- File
Formats: Information about preclustering (.pcl), clustered data
table (.cdt), gene tree (.gtr) and array tree (.atr) files generated
in the process of clustering data
- Cluster
and TreeView Manual from Michael Eisen at Lawrence Berkeley Laboratories
|
|
The Repository allows users to save and exchange retrieved and
analyzed data from the database, such as .cdt and .pcl files. The Repository is
accessed through the web and it allows you to save data on our server
at every step of the data retrieval and analysis pipeline. You can
also analyze and re-analyze the same data sets in various ways making
the comparison of different analyses easier. In addition, you can
share your data files with others in your group or give access
privileges to outside collaborators, as you would with an experiment.
This help page describes how to use the Repository.
|
|
|
|
Each user will have a space quota for the Repository of 200 MB. The
amount of memory used by files currently in your repository is shown
on the bottom of the page. Once you have reached your quota, you will
not be able to save new files to your repository until you delete some
old ones. Therefore we ask that all users curate their own files,
i.e. delete the unnecessary ones to save space. Warning: Once
a file is deleted from the Repository it is lost and we will not be
able to recover the file. If you deleted all the unnecessary files and
you strongly feel you still need more space, please contact us. We can
increase your quota.
|
|
|
|
There are two ways you can access the contents of your Repository. If
you already have files saved into the Repository select the Repository List link from the
main page under the "List Data" section. This link will show
all the files you have in your repository and it will allow you to
navigate to see other users' repository files for which you have
access to view.
You can also see the same Repository list when you save a file in the
repository during data retrieval or analysis.
|
|
|
|
You can make files in your Repository accessible to other database users
and you can see files in other users' repositories to which you have
been given access. In general, access to files the Repository is
controlled the same way as access to experiments is controlled:
members of a default group (lab group) can see each other's repository
without restriction and you can give view access to your files to any
other database user or group.
To give additional access to groups or individual users click on the
respective edit (  )
icon on the right side of the window. On the next page you can either
add or remove access to the file. At this time we don't allow public
access to files stored in the repository.
To access files in the Repository of other users, select a name
from the pull down list after "View the repository of" on the bottom
of the page. Hit the "submit" button and you will see the list of
files available to you in that repository.
|
|
|
|
The top of the page lists whose repository you are in. If it is not
yours, you can always go back to it using the 'MY REPOSITORY'
links. To navigate between Repositories available to you, use the
pull-down menu: "View the repository of", hit submit and you will get
a list of the files you have access to in the selected repository.
The saved files in the Repository can be sorted by any of the column
names that are highlighted. For Example, clicking the 'Size' column
orders the files according to increasing size.
|
|
Upload files
|
You can upload files from your desktop computer to your
repository. You can upload either a .pcl file or a .cdt file together
with .gtr and .atr files if you have them. You can upload by clicking
the 'UPLOAD' link on the right side of the page. Sometimes if
you have a problem during uploading, it is browser specific, because
some browsers randomly add junk onto the beginning or end of a file
when uploading it (thanks Microsoft!). We suggest you try at least
two browsers when uploading before contacting the curators. We have
found Netscape to be more reliable for uploads.
|
| |
The Icons:
|
|
Allows you to look at the selections you made during data retrieval,
filtering, etc.
|
|
 |
You can download the entire file to your computer. The downloaded file
will be compressed (in the .tgz format) and can be unpacked with
Stuffit Expander or similar software. The resulting file is a text
file of the type shown in the table (see the File
Formats help for various formats found in the database).
|
|
 |
After confirmation the file will be deleted. Once a file is deleted it
is lost and cannot be recovered.
|
|
|
You can edit the name and the description of the file, and give access
to other users or groups to see the file.
|
|
 | You
can filter the data that was retrieved from the database. See the Data
Selection for Analysis help for more information on data
selection.
|
|
|
Selecting this icon allows you to perform clustering analysis on the
data. Take a look at the Analysis
Methods help page for more information about clustering methods.
|
|
 |
This icon indicates that the file is a clustered file. Clicking on it
shows you a static 'Cluster Image View' of the cluster.
|
|
 |
This icon indicates that the file is a clustered file. Clicking on it
shows you a static 'Spot Image View' of the cluster. This icon is
available if the spot coordinates were retrieved from the database.
|
|
 |
This icon indicates that the file is a clustered file. Clicking on it
shows you a static 'Joint Cluster and Spot Image View' of the
cluster. This icon is available if the spot coordinates were retrieved
from the database.
|
|
 |
Clicking this icon allows you to look at the file in an interactive
fashion using GeneXplorer.
|
|
|
[an error occurred while processing this directive]
