From LipidomicsWiki

Contents 1 Differential Expression using the B-Fabric Analysis tool 1.1 Workflow Overview for Transcriptomics 1.2 Create an Experiment Definition 1.3 Analyze or Process Data 1.4 Rerun an Analysis

Differential Expression using the B-Fabric Analysis tool

(Functional Genomics Centre Zürich P06 )

Gene array hybridization and analysis are performed at the Functional Genomics Centre in Zürich. Since data acquisition and evaluation are performed in the same unit no transfer of files is necessary for gene array analyses. Samples will be submitted via Dr. Christian Wolfrum, data analysis is performed according to the outlined SPP by each individual partner.

Workflow Overview for Transcriptomics

Registering and annotating samples is straightforward and allows for batch processing. The user has to perform the following steps:

1. Create one sample and one associated extract in B-Fabric for each microarray and annotate them according to the experimental design
2. Inform FGCZ bioinformatics about the finished annotation by email (stefan.zoller@fgcz.ethz.ch or hubert.rehrauer@fgcz.ethz.ch)

Then , FGCZ bioinformatics performs the following steps:

3. Check the annotation and, if necessary, request additional information
4. Import the data into the database and initiate the appropriate first quality control and analysis pipelines

Create an Experiment Definition

Creating an Experiment Definition is useful to group your data (resources, files, etc.) together and extend them with attributes. It is possible to reuse the annotations from the associated samples and extract, but it's also really easy to define new attributes on the fly.

1. Go to your project and click on the "Add Experiment Definition" button
2. Add the resources (files) by first selecting the workunits and then the resources
3. Select the attributes (e.g. Species, Treatment, etc.) that should be included in the experiment definition.
4. Click on the "Save" button
5. Change the attributes and add new columns if needed
6. Click on the "Save" button

Analyze or Process Data

Analyzing data means to run an analysis or experiment on an experiment definition. Depending on the experiment definition (and the files and resources it encloses), different analyzes are available. If an analyze needs additional parameters, you will get a form to enter them on the fly.

1. Select the Experiment Definition that contains the data to analyze or process
2. Select the analysis you would like to run with the experiment definition by clicking on the button on the lower right.
3. You will be asked to enter a name for the analysis result
4. If necessary, you will be asked to define more experiment parameters
5. After clicking the "Save" button, the analysis will be executed

Rerun an Analysis

A workunit that holds the result of an analysis, contains a Rerun Analysis button. This is a convenient method to execute an analysis and mostly allows to change the experiment parameters.

1. To re-run an analysis, just click on the "Re run Analyse" button
2. Change the parameter if necessary
3. After clicking the "Save" button, the analysis will be executed.


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