Second exercise on analyzing gene expression data in qbase+

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In this example we will analyze data from another expression study with the following characteristics:

All samples fit in a single run: Run7
We have the following samples:

  • 5 control samples: control1, control2…
  • 5 treated samples: treated1, treated2…
  • 1 no template control: NTC

The expression of the following genes was measured:

  • 2 reference genes: refgene1 and refgene2
  • 2 genes of interest: gene1 and gene2

There are two technical replicates per reaction

Creating a new experiment

Loading the data

Adding sample annotation

Download the the sample properties file.

Analyzing the data

Look at the target bar charts.

The samples of each group are biological replicates so you might want to generate a plot that compares the average expression of the treated samples with the average expression of the untreated samples.