Process Description

Eland Input Engine

Eland Input Engine imports a set of Eland output files and combines them into a SAS data set, and reduces the total number of reads by binning them and calculating read counts.

Note: This process is considered experimental.

What do I need?

Before you can successfully import the raw data into SAS data sets that can be used for analysis in JMP Genomics, you must locate and gather several sources of information:

•

An Experimental Design File (EDF) that indexes the individual raw data files for the experiment. The EDF is typically a text file or Excel spread sheet and must be created before the data can be imported.

Important: The EDF used for importing Eland data must contain a variable called SampleName. The values listed in this column identify each sample in the experiment. Providing this name allows the Eland data for each sample, which are typically spread across multiple .txt files, to be merged into one SAS data set.

•

All of the Eland .txt files containing the raw data, which must be located and copied to a single folder. Each .txt file corresponds to an individual chromosome and contains the hybridization intensities for that array.

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Output/Results

The output data sets generated by this process are listed in a Results window. Refer to the Eland Input Engine output documentation for detailed descriptions.