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Information about the different output options can be found by selecting the adjacent () icon. 

Detection p-values. This is the confidence score that the signal of a probe was significantly higher than the background defined by negative control probes. Selecting this checkbox produces a spreadsheet ending with '_detectionp' in addition to the spreadsheet containing beta values. Each row of the _detectionp spreadsheet will be a different sample and the sample names will end in '_detectionp'. This spreadsheet can be used to filter out probes that do not show signal above background. 

Probe Intensity. This is the sum of the methlyated and unmethylated intensities per probe. Selecting this checkbox produces a spreadsheet ending with ‘_probe’ in addition to the spreadsheet containing beta values. Each row of the _probe spreadsheet will be a different sample and the file names will also end in ‘_probe.’ The probe intensity values will be log2 transformed by default (note that the beta values are not log2 transformed).

Probe Signal. This option will become available if Probe Intensity is selected. Selecting this checkbox produces a spreadsheet ending with ‘_probe.’ The methylated and unmethylated intensities are shown on separate rows for each sample, in addition to the summed values. The sample names will end in ‘_meth’ or ‘_unmeth’ for methylated and unmethylated values, respectively. The probe intensity values will be log2 transformed by default.

Raw Probe Intensity. This is the sum of the raw red and green signal intensities per probe. Selecting this checkbox produces a spreadsheet ending with ‘_raw’ in addition to the spreadsheet containing beta values. Each row of the spreadsheet will be a different sample and the file names will also end in ‘_raw.’ The raw probe intensity values will be log2 transformed by default.

Raw Probe Signal. This option will become available if Raw Probe Intensity is selected. Selecting this checkbox produces a spreadsheet ending with ‘_raw.’ The red and green intensities will be shown on separate rows for each sample, in addition to the summed values. The sample names will end in ‘_red’ or ‘_green’ for red and green values, respectively. The raw probe intensity values will be log2 transformed by default. 

Antilog Probe Intensity Values. Selecting this checkbox will show the probe intensity data without log2 transformation.

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• Select Probe Intensity and Antilog Probe Intensity Values (Figure 2)
• Select OK to close the Advanced Import Options dialog
• Select Import to import the data and perform the selected normalization method
• Select the (_probe) spreadsheet from the spreadsheet tree
• Delete any samples with _detectionp names
• Create sample attributes, assign samples to the groups, and filter as described in Annotate and filter samples
• Select Transform from the main toolbar 
• Select Normalize to baseline 

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