Annotating a full experiment
[ Main_Page | Exercises on using qbase+ ]
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 |
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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. |
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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 ? |
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The easiest way to look at the data is to open it:
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 |
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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.
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 |
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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:
You can attribute wells to this target in exactly the same way as you did the attribution for samples. |
Now you should have generated the same data set as used in Second exercise on analyzing gene expression data in qbase+.