SummaryStatistics.pdf
Summary Statistics
Overview
The Summary Statistics command will calculate a set of summary statistics for an Omic data object's observations or variables, and generate a new Table with the summary information in the Solution Explorer, under the Summary folder. Optionally, the user can choose a "Group" column, so subsets of the data will be independently summarized.
To run this module, type MicroArray  Summarize  Summary Statistics.
Input Data Requirements
It works on Omic data types.
General Options
Input/Output
 Project & Data: The window includes a dropdown box to select the Project and Data object to be filtered.
 Variables: Selections can be made on which variables should be included in the filtering (options include All variables, Selected variables, Visible variables, and Customized variables (select any pregenerated Lists)).
 Observations: Selections can be made on which observations should be included in the filtering (options include All observations, Selected observations, Visible observations, and Customized observations (select any pregenerated Lists).
 Output name: The user can choose to name the output data object.
Options
 By: Under the Options section, the user can choose to either run Summary Statistics on variables or observations.
 Summarizing by Variables means that, for each variable, the set of observations will be summarized
 Summarizing by Observations means that, for each observation, the set of variables will be summarized
 Group: This dropdown box can be used to choose a column (from the Design Table for summarizing variables, or the Annotation Table for summarizing observations) to group the summarizing criteria. For instance, if the experiment contains a Treatment column, the user may be interested in using this column as a Group by which to summarize, to calculate summary statistics separately for each Treatment group.
 Statistics: This box contains the statistics to be generated by the Summary Statistics command. Multiple selections can be made (hold ctrl to select multiple) and are listed below.
 Quantiles: If Quantiles is selected in the Statistics section, then the Quantiles box can be set to the percentage that is desired by the user.
 Append summary statistics to the covariate table: checking this box will append the newly generated statistics column to the relevant metadata table. This column can then be used in future filtering operations.
 Generate observation box plots: Checking this box will create a box plot based on the summary statistics options selected above.


N 
number of data points 
Mean 
average 
Standard Deviation  
Min 
minimum value in that variable or observations 
Max 
maximum value in that variable or observation 
MinAbs 
minimum absolute value 
MaxAbs 
maximum absolute value 
Range 
range of values in that variable or observation 
NMissing 
number of missing values in that variable or observation 
NMissingPercentage 
percentage of missing values in that variable or observation 
NNotMissing 
number of nonmissing values in that variable or observation 
NNotMissingPercentage 
percentage of nonmissing values in that variable or observation 
Sum 
sum of values for that variable or observation 
variance of values for that variable or observation  
standard error for that variable or observation  
CV 

Median 
median for that variable or observation 
interquartile range for that variable or observation  
skewness for that variable or observation N  
kurtosis for that variable or observation  
median absolute deviation for variable or observation  
NPositive 
Number of positive data points for that variable or observation 
NNegative 
Number of negative data points for that variable or observation 
PositivePercentage 
Percentage of positive data points for that variable or observation 
NegativePercentage 
Percentage of negative data points for that variable or observation 
PositiveChangeSize 
maximal positive value * percentage of positive values for that variable or observation 
NegativeChangeSize 
minimal negative value * percentage of negative values for that variable or observation 
PositiveMean 
average of positive values for that variable or observation 
NegativeMean 
average of negative values for that variable or observation 
mean or average which indicates the central tendency or typical value of a set of numbers  
Quantiles 
Quantile value for that variable or observation, set according to the Quantiles percentage box 
Output Results
This module generates a new Table in the Solution Explorer under the Summary folder. For every Variable or Observation,the selected summaries of Observations or Variables, respectively, will be displayed.
For example, the following table is output from summarizing N (count) and mean By Variable, and grouping the Observations by the design table's Cell Line column.
For each sample group, the N and mean are displayed for each Variable.
OmicScript