Scaling

Rescaling means that you calculate NRQ values relative to a specified reference level.

Qbase+ allows you to rescale the NRQ values using one of the following as a reference:

• the sample with the minimal expression
• the average expression level of a gene across all samples
• the sample with the maximal expression
• a specific sample (e.g. untreated control)
• the average of a certain group (e.g. all control samples): this is often how people want to visualize their results
• positive control: only to be used for copy number analysis

After scaling, the expression values of the choice you make here will be set to 1 e.g. when you choose average the average expression level across all samples will be set to 1 and the expression levels of the individual samples will be scaled accordingly.

How to scale to the average of the untreated samples?

You can specify the scaling strategy on the Scaling page. Select Scale to group and set the Scaling group to the untreated samples . This is one of the reasons why you need the grouping annotation.

Rescaling to the average of a group is typically used to compare results between 2 groups, e.g. treated samples against untreated controls. After rescaling, the average of the NRQs across all untreated samples is 1 and the NRQs of the treated samples are scaled accordingly.

Click Next to go to the Analysis page.