source: orange-bioinformatics/docs/rst/PIPA.rst @ 1873:0810c5708cc5

Revision 1873:0810c5708cc5, 1.9 KB checked in by Ales Erjavec <ales.erjavec@…>, 7 months ago (diff)

Moved '_bioinformatics' into orangecontrib namespace.

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1.. _pipa:
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3PIPA
4====
5
6.. image:: ../../orangecontrib/bio/widgets/icons/PIPA.png
7   :alt: Widget icon
8   
9Signals
10-------
11
12Inputs:
13   - None
14
15Outputs:
16   - Selected microarrays (ExampleTable)
17        Selected experiments. Each annotated column contains results of a single experiment or, if the corresponding option is chosen, the average of multiple replicates.
18
19Description
20-----------
21
22.. image:: images/PIPA.*
23   :alt: PIPA widget
24
25The PIPA widget lists accessible experiments, which can be filtered with the "Search" box at the top. The selected experiments will appear on the output when the "Commit" button is clicked. You can connect the output of the PIPA widget to any Orange widget which accepts ExampleTable as input. The widget will automatically save (cache) downloaded data and you will therefore be able to analyse them offline.
26
27To select multiple experiments click them while holding the "Control" key. For frequent combinations of selections use the "Experiment Sets" feature: select experiments and click on the "+" button.
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29The logarithmic transformation is computed as the binary logarithm of the (value + 1). If username and passwords are not given, only the public experiments will be accessible.
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31Examples
32--------
33
34In the schema below we connected PIPA to Data Table, GO Enrichment Analysis, and Distance Map (through Attribute Distance) widgets.
35
36.. image:: images/PIPA_schema.*
37   :alt: Example schema with PIPA widget
38
39The Data Table widget below contains the output from the PIPA widget. Each column contains gene expressions of a single experiment. The labels are shown in the table header.
40 
41.. image:: images/PIPA_datatable.*
42   :alt: Output of PIPA in a data table.
43
44The Distance Map widget shows distances between experiments. The distances are measured with Attribute Distance widget, which was set to compute Pearson distances (as (1-PearsonCorrelation)/2).
45
46.. image:: images/PIPA_distance.*
47   :alt: Distances between experiments.
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