LEM: Linear Expression Map

Parameter Information


These initialization parameters are used to direct MeV to information about the nature of the arrayed spots and the sampled genome. The parameters that are selected in this dialog will determine the Linear Expression Map that is produced. Incorrect selections will produce maps that are not correct. If a map looks unusual you can check the entered parameters in the LEM Mapping Summary node on the result tree.

Locus Identifier Selection

This menu provides a list all spot annotation fields in MeV. Select the annotation field that should be used to map each spot to an associated locus.

Coordinate Data Selections

Use Coordinate File
This option, when selected, indicates that chromosome location and coordinate information will come from an auxilliary file. The format of this file is shown in the manual section for LEM. The coordinate file is a text tab delimited format file that contains no header and 3 or 4 columns.
< locus_id > [chromosome_id] < 5'_end > < 3'_end >

The second column, chromosome_id is only needed if the organisim under study has multple chromosomes.

Multiple Chromosomes
If selected, this option indicates that there are spots from loci on multiple chromosomes on the array. When selected the information to map loci to chromosomes is expected to be in the input file or within an annoation field if the coordinate file is not used. If not using a file one should indicate which field of spot annotation corresponds to chromosomal membership information. (mapping spots to chromosomes)

Coordinate Information
If not using a coordinate file, these menus are used to select annotation fields that indicate 5' and 3' ends of the locus.