If your experimental design includes a sample or a group of samples serving as a baseline control, you can normalize the experimental samples by subtracting or dividing by the baseline sample(s) using the Normalize to baseline task in Partek^® Flow^®Partek Flow. For example, in PCR experiments, the delta Ct values of control samples are subtracted from the delta Ct values of experimental samples to obtain delta-delta Ct values for the experimental samples. 

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There are three options to choose the baseline samples:

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To normalize data to all the samples, choose to calculate the baseline using the mean or median of all samples for each feature, and choose to subtract baseline or ratio to baseline for the normalization method (Figure 2), and click Finish.

Use a group of sample to create baseline

When there is a subset of samples that serve as the baseline in the experiment, select use group for Choose baseline samples.  The specific group should be specified using sample attributes (Figure 3).

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

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