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Choose this option use group, select the attribute containing the baseline group information, e.g. Treatment in this example, with the samples labeled as Control will be with the group Control for the Treatment attribute used as the baseline. The control samples can be filtered out after normalization by selecting the Remove baseline samples after normalization check buttonbox.

Use matched pairs

When using matched pairs, one sample from each pair serves as the control. An attribute specifying the pairs must be selected in addition to an attribute designating which sample in each pair is the baseline sample (Figure 4). 

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After normalization, all values for the control sample will be either 0 or 1 depending on the normalization method chosen, so we recommend removing baseline samples when using matched pairs. 

The output of Normalize to baseline is a Normalized counts data node.