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Agilent GeneSpring

In the GenomeQuest RNA-Seq workflow, we provide spreadsheets that can be imported in GeneSpring for analysis.

GeneSpring provides statistical tools for fast visualization and analysis of expression data. It's an interactive desktop software for statistical analysis of microarray and RNA-Seq expression data within a biological context. For more information about GeneSpring, Click here
Example of a GenomeQuest RNA-Seq experiment imported in GeneSpring

Importing a GenomeQuest RNA-Seq spreadsheet into GeneSpring

The first time you import a GenomeQuest RNA-Seq experiment into GeneSpring, you need to create a new GeneSpring "Technology".
It will allow GeneSpring to recognize the layout of the GenomeQuest spreadsheets.
Important: You only need to do that once if you import spreadsheets with the same number of samples, but you'll need to create a new technology if you import spreadsheets with a different number of samples.
In the future, GeneSpring (> GX 10) will automatically recognize the layout without the need of creating a new technology.
Contact us at support@genomequest.com if you are having trouble creating a new technology.

Creating a new Experiment

The first step is to download the spreadsheet from your GenomeQuest experiment

You need to create a new Project, or open an existing one in GeneSpring.

Select Project > New Experiment

Give a meaningful name to your experiment, and make sure you select Generic Single Color for the Experiment Type, add a description if needed, then click Next

Select the Technology for GenomeQuest you created (If haven't done that, see below, select your GenomeQuest spreadsheet, called "genespring.txt" (Choose File), then click Next

Select your Normalization (or none), then click Next

Select your Baseline option, then click Finish

You should see your new Experiment in the list

Creating a GQ technology in GeneSpring

The first step in GeneSpring is to define the GQ spreadsheet layout that will be applied to files imported from GQ. Note that depending on the type of experiment you ran in GenomeQuest, you might need to create several technologies (one per spreadsheet layout, depending on the number of samples). This is necessary because GeneSpring require each technology to be based on a set number of columns.

In the future, GeneSpring (> GX 10) will automatically recognize the layout without the need of creating a new technology. Contact us at support@genomequest.com if you are having trouble creating a new technology.

To create a technology in GeneSpring, you need to download the spreadsheet of the experiment from the GenomeQuest RNA-Seq report page, as shown below

In GeneSpring:

Create or Open a project

In Annotation > Create Technology, select Custom From File, and click Next

in Step 1: Give a meaningful name to the technology, select Single Color, select the spreadsheet you downloaded from GenomeQuest for sample and annotation, and click Next, as shown below