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IPA info

This page contains information related to the usage and troubleshooting of Ingenuity programs, such as Ingenuity Pathways Analysis (IPA, from http://www.ingenuity.com)

1. Using IPA at the UEB Servers

First you need to connect to one of the UEB Servers. See:
http://ueb.vhir.org/external
Considering that you are going to access for using IPA

Once you are logged in the server (with user vhir and your own password), you will see a desktop like the following:

Fes clic per ampliar
Fes clic per ampliar


You can launch the IPA program double clicking at the corresponding icon in the desktop. If you see any message offering you to update Java (like in the image below), select the option "Do not ask again until the next update is available", please, and click at the button "Later", since it is the UEB Staff who needs to update Java in the server to have it successfully updated for all users. We will appreciate if you send us a message warning us about that java update warning.

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Fes clic per ampliar


Then you may see a pop up window asking you to accept to run the Java application. Please click at "Run".

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Fes clic per ampliar


Provide the IPA credentials that you have been indicated, for the email uebsol at vhir.org (since March 2016, ueb at vhir.org ACCOUNT IS NOT WORKING!)

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Fes clic per ampliar


Once succeeded, you should see a message indicating that the connection to the IPA server succeeded and that it's Retrieving data...

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Fes clic per ampliar


Then you will see a welcome message from IPA (something like this one in the image below):

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Fes clic per ampliar


Do your analysis normally.

Once you are finished, click at "Close IPA" at the top right corner of the application, and select to "Clear any remembered password" in the confirmation dialog that you will be shown.

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Fes clic per ampliar


Once you are finished with the connection at the UEB server, logout from the Server through the icon that you will see at the bottom right corner of the desktop.

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Fes clic per ampliar


Contact us if you have any issue or question.

2. Error messages

2.1. At login time: Concurrency limit reached

It may happen that IPA complains at login time that we have already reached the maximum quota of allowed concurrent users (or something similar).

Example of error message in these cases (while the user was working normally with IPA, using Windows Vista). The error message is shown before fully loading IPA, and not while working with the loaded application.

Image

Similar errors can be shown with other operating systems:

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Solution:

If we know for sure that no other people is connected at that specific moment, we can probably solve it by means of clearing the java cache in the browser from our computer, and try again.

Quote:
To resolve the issue you have reported we recommend clearing the Internet Browser cache and Java cache on your computer. Please follow the steps below.

Step 1: Clear Browser Cache

Internet Explorer 7 and 8:
1. Go to the Tools menu Internet Options.
2. On the General tab, in the Browsing history section, click on the “Delete” button. This will open the Delete Browsing History dialog box. In this, select Temporary Internet files and Cookies. Then click on the “Delete” button.

Firefox:
1. Go to the Tools menu Clear Private Data.
2. In the Clear Private Data dialog box, select Cache and Cookies and click on "Clear Private Data Now".

Step 2: Clear Java Cache

Java 1.6.0:
1. Go to the Windows Start menu Control Panel. In the Windows Control Panel, double click on the Java icon. This will open the Java Control Panel.
2. At the bottom of the Java Control Panel window, in the Temporary Internet Files section, click on the "Settings" button. This will open the Temporary Files Settings dialog box.
3. In the Temporary Files Settings dialog box, click on the "Delete Files" button.
4. Select all boxes in the Delete Temporary Files box and click "OK".

Please let us know if this does not help resolve the problem you are encountering.


Here you can also see some screenshots about clearing the Java Cache as indicated in the previous instructions (example from Ubuntu 12.04)
Image
Image
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2.2. More network errors while in VHIR or VHIO? Set up the proxy information in Java also

See the following document, and wherever it says proxy, set the proxy information for VHIR:
url: http://conf_www.ir.vhebron.net
port: 8081

Image proxy_settings_ipa_8.pdf

3. Some tips for setting up a core analysis

Notice that this is just a chunk of notes that could be useful to launch a core analysis with data coming from UEB's gene expression analysis pipeline.
For more detailed info on this and any other case, please, follow the help documentation and tutorials that could be found within IPA software.

Preparación de los datos y análisis
  • A partir de los archivos ExpresAndTop.csv obtenidos en la UEB
    • cambiar la separación por punto y coma a separación por tabuladores
    • cambiar la separación de decimales de coma a punto
  • Cargar los datos en el IPA y comprobar que se han cargado bien (se tienen que apreciar distintas columnas, bien separadas, y en gris)
  • Seleccionar "Flexible Format" como "1. Select File Format"
  • Dejar (habitualmente) en "Yes" la opción de "2. Contains Column Header"
  • Seleccionar "Affymetrix" (o lo que toque) como "3. Select Identifier Type"
  • Seleccionar el tipo de array utilizado en "4. Array platform used for experiments"
  • Elegir la columna de identifadores de Affymetrix como "ID"
  • Elegir las columnas de:
    • logFC como "Observation 1- log ratio"
    • adjPvalue como "Observation 1 - False discovery Rate"
  • Salvar y continuar (dándole al botón de "Analize/Filter dataset" y eligiendo "Core Analysis" o lo que se quiera...)
  • Dejar la mayoría de opciones por defecto y simplemente cambiar la especie utilizada, y si quiere, especificar relaciones directas o directas+indirectas
  • Adjustar los valores de logRatio y FDR de manera que nos queden unos 200-300 genes (unos 100-200 mínimo, unos 800-900 máximo)
  • Darle a "Run analysis"

4. More questions?

Contact us
Statistics and Bioinformatics Unit. Vall d'Hebron Research Unit.
http://ueb.vhir.org
Ph. +34 934894007