wiki:xQTLBiologistBrowse

TracNav(xQTL)?

xQTL workbench - Browse or search available data

Start by exploring the data by click on Browse data in the main menu. This will take you to a screen with four tabs, which are explained in more detail below.

Overview

  • The first tab named Investigation overview will present you with a summary view of all entries in this investigation.
  • You can change investigations with the arrowed buttons at the top.
  • The information for a single investigation is gathered once and then cached. Use Refresh to reload the information.
  • Clicking on a type of data will take you there. This is a shorthand: you can always browse to all datatypes using the tabs Data matrices and Annotations.
  • Similarly, the Browse button is a shorthand to be taken to the tabs of this data category (data, annotations or file) where you can start adding data with the Add new record button.
  • The default view will display 4 entries for each type: use Show all to expand.

View data

  • This tab allows you to add, view and remove data matrices. These are rectangular pieces of (raw) experimental data accompanied by row- and column names.
  • Matrices themselves are annoted with the 'Data' entries, while their row- and column entries are annotated as separate (strong) datatypes found in the Annotations tab.
  • There are a number of plugins that will help you deal with matrices:
    • View = Uploads data and views the numerical/textual data.
    • Inspect = Check whether annotations are missing.
    • Delete = Delete source data linked to this Data entry.

View annotations

  • This section allows you to add, view and remove annotations such as Individual, Gene or Marker.
  • These annotations are often linked to a data matrix, but they don't have to be.
  • You can view display a list of records which is manipulatable using the View menu, search box, or paging buttons.
  • When clicking edit record you can change the values of a record.
  • Click More annotions to see more exotic data types such as DerivedTrait or EnvironmentalFactor.

View files

  • Found under Upload data in the main meny, here you can add files in their original form to the database.
  • Files are coupled to an investigation. That is why they also appear in the Investigation overview.
  • Specify the name and extension of the file in a standard record. Try making a file named 'test' with extension 'txt'. Save the record.
  • You will now see an upload window. Files can be added by selecting them from your filesystem, or by typing in the text area. Try typing 'this is my file', and press the lower-right Upload button.
  • A viewer will serve out the contents based on the extension. A photo (e.g. PNG) will result in a visible picture. Text is rendered as plain (non editable) text.
  • Using the delete current record button will remove the file entry and the associated file.
  • Files with extension 'FIG' (an R plot format) will be rendered by a special applet. You might need to install Java in your browser to view it.
Last modified 6 years ago Last modified on 2012-02-14T16:12:49+01:00