SAS Scientific Discovery Solutions Analytical Processes

Folder Products Analytical Process Name Input Data Format PROC(s) Used

Annotation

Microarray

Create Gene Annotation (AP)

File containing a column of gene identifier

REGISTRYIMPORTSORT

Design

Microarray, Proteomics

Experimental Design 1-Way

N/A

PLANOPTEXTRANSPOSEPRINT

Design

Microarray, Proteomics

Mixed Model Power

Stacked

MIXED

Genetics

Marker

Case_Control Association

Input data: 2 columns per marker, 1 row per individual.

Annotation data: 1 row per marker

CASECONTROLPSMOOTHSORTPRINT

Genetics

Genetic Marker

Haplotype Estimation

Input data: 2 columns per marker, 1 row per individual.

Annotation data: 1 row per marker

HAPLOTYPEPSMOOTHSORT

Genetics

Genetic Marker

Haplotype Trend Regression

Input data: 2 columns per marker, 1 row per individual.

Annotation data: 1 row per marker

HAPLOTYPELOGISTICREGSORTPRINTTRANSPOSE

Genetics

Genetic Marker

Linkage Disequilibrium

Input data: 2 columns per marker, 1 row per individual.

Annotation data: 1 row per marker

ALLELESORTSUMMARYPRINT

Genetics

Genetic Marker

Marker Properties

Input data: 2 columns per marker, 1 row per individual.

Annotation data: 1 row per marker

ALLELESORTTRANSPOSE

Genetics

Genetic Marker

Phenotype Summary

SAS data set

SORTFREQ

Genetics

Genetic Marker

Quantitative TDT

Input data: 2 columns per marker, 1 row per individual.

Annotation data: 1 row per marker

ALLELEPSMOOTHMIXEDGLMREGUNIVARIATESORTPRINT

Genetics

Genetic Marker

Quantitative Trait Association

Input data: 2 columns per marker, 1 row per individual.

Annotation data: 1 row per marker

ALLELEPSMOOTHMIXEDGLMREGSORTPRINT

Genetics

Genetic Marker

TDT

Input data: 2 columns per marker, 1 row per individual.

Annotation data: 1 row per marker

FAMILYPSMOOTHSORTPRINT

Input Engines

Genetic Marker

Arlequin Input Engine

Arlequin format (*.arp)

SORT

Input Engines

Genetic Marker

NEXUS Input Engine

NEXUS format (*.nex)

 

Input Engines

Genetic Marker

Pedigree Input Engine

Various types of pedigree data

IMPORTSORT

Input Engines

Microarray

Affymetrix Input Engine

Design Table

Affy CEL version 3 (*.cel)

Affy CEL version 4 (*.cel

Affy CHP (*.chp)

DATASETSREGISTRYIMPORTSORT

Input Engines

Microarray

Agilent Input Engine

Design Table

Agilent raw file (*.txt)

DATASETSREGISTRYIMPORTSORT

Input Engines

Microarray

GenePix Input Engine

Design Table

Genepix raw file (*.gpr)

DATASETSREGISTRYIMPORTSORT

Input Engines

Microarray

QuantArray Input Engine

Design Table

QuantArray raw file (*.txt)

DATASETSREGISTRYIMPORTSORT

Input Engines

Microarray

ScanAlyze Input Engine

Design Table

ScanAlyze raw file (*.dat)

DATASETSREGISTRYIMPORTSORT

 

Input Engines

Research Data Management (RDM)

Data Import Input Engine

Tab, CSV, Excel, SAS, space-delimited

 

DATASETSREGISTRYIMPORT

Input Engines

RDM

Experiment Input Engine

Design Table

Tab, CSV, Excel, SAS, space-delimited

DATASETSREGISTRYIMPORTSORT

Normalization

Microarray

Loess Normalization

Stacked

LOESSMEANSSORTDATASETSAPPENDTRANSPOSE

Normalization

Microarray

Quantile Normalization

Stacked

MEANSSORT

Normalization

Microarray, Proteomics

Mixed Model Normalization

Stacked

MIXEDMEANSSORT

Normalization

RDM

Data Standardize

Stacked

STDIZE

Pattern Discovery

Microarray

Hierarchical Clustering

Rectangular, rows are clustered

TRANSPOSE

Pattern Discovery

Microarray

K-Means Clustering

Rectangular, rows are clustered

TRANSPOSE

Pattern Discovery

Microarray, Proteomics

Distance Matrix

Rectangular, distances between rows are calculated

%DISTANCESORT

Pattern Discovery

Microarray, Proteomics

Multidimensional Scaling

Square (distance matrix)

MDSSORT

Pattern Discovery

Microarray, Proteomics

Principal Components

Rectangular, principal linear combinations of the columns are computed, and scores are displayed for each row

PLSGLMMODTRANSPOSE

Quality Control

Microarray

Array Pseudo Image

Stacked

STDIZEUNIVARIATEMEANSDATASETSAPPENDSORTTRANSPOSE

Quality Control

Microarray, Proteomics

Array Group Correlation

Stacked

SURVEYSELECTSORTTRANSPOSE

Quality Control

Microarray, Proteomics

Surface Summary

Stacked

KDEUNIVARIATEMEANSSORTFORMATG3D

Quality Control

RDM

Ratio Analysis

Stacked

LOESSMEANSSORTCONTENTS

Spectral Analysis

Proteomics

Spectral Bin

Rectangular, with samples as columns

MEANS

Spectral Analysis

Proteomics

Spectral Detrend

Rectangular, with samples as columns

TRANSPOSE

Spectral Analysis

Proteomics

Spectral Peak Find

Rectangular, with samples as columns

IMLSORTTRANSPOSE

Spectral Analysis

Proteomics

Spectral Plot

Rectangular, with samples as columns

TRANSPOSE

Statistical Modeling

Microarray, Proteomics

Discriminant Analysis

Rectangular, with predictors and class as columns

TRANSPOSE

Statistical Modeling

Microarray, Proteomics

Mixed Model Analysis

Stacked

MIXEDMULTTESTMEANSSTDIZEDATASETSCONTENTSSORTTRANSPOSEPRINT

Statistical Modeling

Microarray, Proteomics

Partial Least Squares

Rectangular, with Xs and Ys as columns

PLSGLMMODTRANSPOSE

Statistical Modeling

Microarray, Proteomics

Partition Trees

Rectangular, with predictors and Y as columns

TRANSPOSE

Utilities

RDM

Data Contents

Any SAS data set

CONTENTSPRINT

Utilities

RDM

Data Correlation

Rectangular

CORRTRANSPOSE

Utilities

RDM

Data Export

Any SAS data set

EXPORT

Utilities

RDM

Data Filter

Stacked

MIXEDCORRMULTTESTMEANSDATASETSCONTENTSSORT

Utilities

RDM

Data Merge

Any SAS data set

SORT

Utilities

RDM

Data Rank

Any SAS data set

RANKSORT

Utilities

RDM

Data Sort

Any SAS data set

SORT

Utilities

RDM

Data Step

Any SAS data set

 

Utilities

RDM

Data Summary

Any SAS data set

SORTSUMMARY

Utilities

RDM

Data Transpose

Stacked

MEANSSORTTRANSPOSE

Utilities

RDM

Data Transpose Rectangular

Any SAS data set

SORTTRANSPOSE