Output Description

Create a Design File from MiniML

Running this process for the GSE6930_family.xml.tgz compressed data set (downloaded from the GEO FTP server) generates the .txt file shown below. Refer to Create a Design File from MiniML for a description of the output data and files generated by this process.

Experimental DesignFile: This output .txt file provides information about how an experiment is carried out. It defines experimental variables such as treatment conditions and covariates and provides the basis for organizing and analyzing your data. Note that the EDF shown above contains the following four elements required for use in JMP Genomics:

1

The first row of the file must contain column heading names, and the second and subsequent rows must contain data with no blank rows.

2

One column must have header name Array, Chip, or Spectrum. An optional second column must be named Channel or Dye. The data entries in these two columns must uniquely identify the rows of the file. The Create Array Index process helps you generate this column.

3

One column must have header name File or FileName. The entries in this column must contain the names of the raw data files that are associated with each row. The Check File Names process helps you check the accuracy of the filenames.

4

One column must have header name ColumnName. The entries in this column must correspond to the names of the SAS variables in the tall data set that is to be associated with this experimental design. SAS variable names have certain restrictions. The Create ColumnName process helps you generate this column.

In the example shown above, the names of the 68 raw data files are listed in the File column. They are indexed according to the Array and ColumnName columns. Additional columns describe experimental details.

Refer to Experimental Design File (EDF) for more information.