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Usage  
Helps to use HiTS
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Updated May 29, 2009 by aborgabor

Usage

After you have installed all dependencies and the HiTS plugins you are almost ready to use this program. (We are assuming you have set the proxy settings if you need them in one of the previous steps.)

Additional preparations

If you want to use the CellHTS2, or biomaRt Annotator node, you have to start Rserve.

Starting KNIME

When you are analysing large experiments your default memory size set for KNIME may be not enough. In that case you should increase the memory, by changing the line starting with -Xmx in your knime.ini file. -Xmx1024M is not a bad choice if your computer has enough physical memory installed.

You might want to add -Dknime.expert.mode=true to your knime.ini file. This will allow you to use the Dendrogram with Heatmap node, and the looping support of KNIME. It also allows you to select custom normalisation/scoring methods too.

After this you can start your KNIME installation.

Configure your preferences

After you have started KNIME you should see (in your default KNIME perspective) the HiTS nodes in the Node Repository.

You can customise your preferences in the File/Preferences... menu. There you can find KNIME/HiTS Preferences. On that page you have several options:

  • Use names instead of numbers for channels - If selected, your CellHTS2 nodes will give their results in HTML files and node outports with the parameter names collected from the xls files instead of the not too descriptive ch_1, ... names. The usage of this option depends on the Use TCD extension? option. It must be checked if you want parameter names.
  • Use TCD extension? - This option allows you to analyse multiple parameters in one run. The results in HTML files will be from left to right.
  • Column order - In this area you may select which results in which order you want to get in the topTable.txt, and the outports of CellHTS2 node. You may get more information on this page.

The usage of the nodes is similar to the other KNIME nodes. You can get more help on their Node Description views, or the wiki pages listed below:

  • CellHTS2 - calls CellHTS2 and generates HTML report; the statistics are also available on the outports. (You need a running Rserve on your computer with cellHTS2 installed.)
  • Importer - reads some xls files generated by IN Cell Analyser 1000, and if set adds gene symbols/ids from a tab separated file.
  • Simple Configurator for CellHTS2 - reads the plate configuration and the description from different files.
  • biomaRt Annotator - adds BioMart annotations to the results based on the selected preferences and the given gene ids. (It is using the biomaRt R package.) (You need a running Rserve on your computer with biomaRt installed, also internet access.)
  • Heatmap - allows you to visualise the results of your analysis in a plate based view.
  • Rank - gives ranks to your selected parameters' selected statistics.

Common use cases

This page shows some usecases of the program with KNIME.

Try it

You can find workflows in this folder's subfolders if you want to try this without problems. For sample data check this folder. Sample data created with Amanda Birmingham's NoiseMaker program.

Reporting Bugs, Request Features

If you encounter a bug, please report it at this page. It is also for feature requests. Please be so kind if you see the same request or bug there then just star it. Thank you.

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