Import

Experimental Design File

Affymetrix

Illumina

Nanostring

Other Expression

Other Genetics

Proteomics

Next-Gen Sequencing

Text

Summarize

Click on a subcategory to reveal individual import processes.

Subcategory	Contains processes for...	Input data requirement1
Experimental Design File	Creating an Experimental Design File (EDF) for use in other processes.	Raw data files or an existing SAS data set.
Affymetrix	Importing Affymetrix data into SAS data sets.	Raw data files and/or an EDF, for most.
Illumina	Importing Illumina data into SAS data sets.	An Exported or Final Report file.
Nanostring	Importing and normalizing a set of Nanostring files and combining them into a single SAS data set.	Raw data files and an EDF.
Other Expression	Importing other expression data into SAS data sets.	Raw data files and an EDF.
Other Genetics	Importing other genetics data into SAS data sets.	A vendor-specific data file.
Proteomics	Importing proteomics data into SAS data sets.	Raw data files and an EDF.
Next-Gen Sequencing	Generating or binning counts, inferring gene structure, and creating and importing variant call format (VCF) files.	Raw data files. Some require an EDF.
Text	Importing raw data or an existing experiment into SAS data sets.	Raw data files. One requires an EDF.
Summarize	Binning intensities or counts, or constructing a gene model summary.	Tall SAS data set. One requires a gene model text file.

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1

Following the import of data (an Experimental Design File (EDF) is sometimes required), Tall and Wide Data Sets (which are SAS Data Sets) are the most common primary Input Data Sets required throughout JMP Genomics. Less common are stacked, square, and other specialized varieties. (See Other Types of Data Sets.) In many cases, an additional Experimental Design Data Set (EDDS), Annotation Data Set, or settings file is either specifiable or required. See Data Sets Used in JMP Genomics Processes and the documentation for individual processes for additional information.

See the JMP Genomics Starter for other process categories.