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:
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:

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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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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

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.
Ph. +34 934894007