Annotating a full experiment

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In this exercise we will use data coming from the same experiment as the data set in Second exercise on analyzing gene expression data in qbase+. So there you can find a full description of the experiment.

Creating a new experiment

Create a new Experiment called FullAnnotation in Project1
You can find the details on how to create a new experiment in Creating a project and an experiment

Loading the data

Import Run8. This file is in qBase format.
You can find the details on how to import the data file in the Loading the data into qbase+ section of Analyzing data from a geNorm pilot experiment in qbase+

Close the Analysis wizard by clicking the Close wizard button and look at the data.

Is the data annotated ?
The easiest way to look at the data is to open it: Expand Runs in the Project explorer Double click Run8 As you can see, the file does not contain any annotation, which means you will have to add the annotations yourself.

Annotating the data

In the data set, samples are ordered according to the columns:

• control1 is located in column1
• control2 is located in column2
• ...

There are 5 control samples and 5 treated samples.

Annotate the samples
In the Sample section of the Run window select <New Sample>: This opens the New Sample window, where you can specify a name and the type of the sample: Enter the name of the sample, Control1 and click Finish. To attribute wells to this sample: Select the wells in the first column of the data file Select Control1 in the Sample section Do this for all the samples.

In the data set, targets are ordered according to the rows:

• refgene1 is located in row A
• the technical replicate of refgene1 is located in row B
• refgene2 is located in row C
• the technical replicate of refgene2 is located in row D
• ...

There are 2 reference genes and 2 genes of interest. There are two technical replicates of each reaction.

Annotate the genes
In the Target section of the Run window select <New Target>. This opens the New Target window, where you can specify a name and the type of the target: Enter the name of the target: refgene1 set Target type to Reference target click Finish You can attribute wells to this target in exactly the same way as you did the attribution for samples. Do this for all the targets.

Now you should have generated the same data set as used in Second exercise on analyzing gene expression data in qbase+.