Baseline Quantification

Use this parameter to specify the statistics for quantifying the baseline across columns in the Input SAS Data Set (or the specified Baseline Reference SAS Data Set ) for measurements with the same rank.

Statistics for quantifying the baseline are described in the table below:

Statistic	Description
Geometric Mean	Constructs the baseline using the geometric mean across all of the data columns. This option should be selected for non-log transformed count data.
Arithmetic Mean	Constructs the baseline using the arithmetic mean across all of the data columns. This is the default option of quantile normalization .
Median	Constructs the baseline using the median across all of the data columns. This option should be selected for count data 1 .
Upper Quartile	Constructs the baseline using the upper quartile across all of the data columns. This option should be selected for count data.

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1

Bullard, JH., E. Purdom, KD Hansen, and S. Dudoit. 2010. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11:9.