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Changing Your User Preferences

 

Overview

This facility allows GeneLinkerô to remember your preferences from one session to the next.

 

Actions

1. Select Preferences from the Tools menu. The User Preferences dialog is displayed.

 

2. Click the General tab to display the general preferences pane.

3. Set the parameters.

Element

Description

User Name

Your user identifier that appears in annotations and reports containing annotations.

Web Browser

The path to your preferred HTML browser.

Enable automatic visualizations

If this checkbox is checked then whenever any analysis experiment (any experiment other than data import, normalization, filtering, or missing value estimation) completes, the default visualization that is associated with the experiment will be opened automatically as soon as the experiment completes.  By default this preference is checked.

Enable Shared Selection

If this checkbox is checked, items such as genes and samples that are selected in one visualization will also be highlighted in other visualizations.  By default this preference is checked.

PCA Components to Display

The default number of principal components to display in a loadings line plot or loadings color matrix plot (display only - does not affect the calculation).

Histogram Bins for Summary Statistics

The default number of bins for the Summary Statistics chart.

 

4. Click the Gene Database tab to display the gene database pane.

5. Set the parameters.

Element

Description

Gene Display Name

The default type of gene identifier used for display.

Lookup Gene Database URL: Affymetrix

Database URL for looking up a gene with an Affymetrix gene identifier. See Affymetrix URL Format below.

Lookup Gene Database URL: GenBank

Database URL for looking up  a gene with a GenBank gene identifier. See GenBank URL Format below.

Lookup Gene Database URL: UniGene

Database URL for looking up  a gene with a UniGene gene identifier. See UniGene URL Format below.

Lookup Gene Database URL: Custom

The URL used to access another gene database. Use the correct URL format for the database you are accessing.

 

6. Click OK to save changes to the settings or click Cancel to keep the previous values.

For more information about forming query strings, refer to Linking to PubMed and other Entrez databases: http://www.ncbi.nlm.nih.gov/entrez/query/static/linking.html

 

Affymetrix URL Format:

 

GenBank URL Format:

Note the use of the term PPSI_ID. This term must appear in the URL. The application will replace this term with the identifier of a gene.

For example, if the gene being queried has the identifier AF098020, then the application will use the following URL to obtain information about that gene:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&term=AF098020&db=Nucleotide&doptcmdl=GenBank

 

UniGene URL Format:

Note: the use of the terms PPSI_ORGANISM and PPSI_ID. These terms must appear in the URL. The application will replace these terms with the appropriate components of a UniGene gene identifier.

For example, if the gene being queried has the UniGene identifier Ht.9573, then the application will use the following URL to obtain information about that gene:

http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Ht&CID=9573

 

Related Topics:

Lookup Gene

Principal Component Analysis

Summary Statistics