Secondary Annotation Chromosome Variable

Use this field to specify the variable whose values indicate the chromosome on which the SNPs or probesets are located.

This variable is specified here when this information is not included in the input data set.

When this variable is specified along with the position variable, the output negative log p-values are plotted by chromosome and position.

To Specify a Secondary Annotation Chromosome Variable:

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Specify the Secondary Annotation SAS Data Set.

All of the variables in the specified annotation data set are displayed in the Available Variables field.

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Examine the list of available variables.

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Highlight the variable listing the chromosome on which each marker is located.

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Click to add the highlighted variable to the Secondary Annotation Chromosome Variable field, as shown below: