Affymetrix® GRD Data File Format

GRD FILE

Description

The GRD (grid) file stores the estimate of the sub-pixel location of the center of every feature in an array.

Format

The format of the GRD file is a binary file with data stored in big-endian format.

The file consists of the following sections (in order)

Header Section

The file header consists of 36 bytes in total. The values are:

Item DescriptionType Size
1 Magic number used to identify the file:

(octal) 211 107 122 104 015 012 032 012
(hexadecimal) 89 47 52 44 0d 0a 1a 0a
(ASCII C notation) \211 G R D \r \n \032 \n

 char[8]8 byte
2 The version number of the file. The version number is set to 1. float 4 bytes
3 The number of features in the x direction (Nx).unsigned int 4 bytes
4 The number of features in the y direction (Ny).unsigned int 4 bytes
5 The x-direction feature pitch.float 4 bytes
6 The y-direction feature pitch.float 4 bytes
7 The x-direction feature setback. float 4 bytes
8 The y-direction feature setback. float 4 bytes

Tag-Based Header Section

This section contains parameters stored as name/value pairs.

Item DescriptionType Size
1 Total number of bytes in the tag-based header. unsigned int4 bytes
2 Total number of name-value pairs in the tag-based header. unsigned int 4 bytes
3 A series of ASCII strings in a name-value pair format. For each name-value pair we have the following 4 entries:
  • String length of name including the null terminating character, unsigned integer (4 bytes)
  • A null terminated array of ASCII characters with length as specified above.
  • String length of value including the null terminating character, unsigned integer (4 bytes)
  • A null terminated array of ASCII characters with length as specified above.
see description see description

Note: The following tags shall be included in version 1 of the format:

  • "Parent DAT File" - the full name of the DAT file associated with this GRD.
  • "Scan Date Time" - the date and time of the scan from the DAT file.
  • "Scanner ID" - scanner ID from the DAT file.

Optimized Sub-Grid Corner Location Section

The optimized sub-grid corner location section shall contain the corner coordinates of each sub-grid as computed during the DAT file analysis. Note: not all DAT file analyses in GCOS will produce a GRD file.

Item DescriptionType Size
1 Total number of bytes in this section. unsigned int4 bytes
2 Total number of subgrids in this section. unsigned int 4 bytes
3 For each sub-grid the following coordinates are stored:
  • upper left x, float (4 bytes)
  • upper left y, float (4 bytes)
  • upper right x, float (4 bytes)
  • upper right y, float (4 bytes)
  • lower left x, float (4 bytes)
  • lower left y, float (4 bytes)
  • lower right x, float (4 bytes)
  • lower right y, float (4 bytes)
Array of floats #sub-grids * 32 bytes

Feature Center Data Section

The feature center data block consists of Nx * Ny pairs of (x,y) coordinates. Every feature on the array is contains an associated (x,y) feature center.

Item DescriptionType Size
1 The first sub-pixel coordinate pair stored is for the feature at cell-coordinate (0,0). float, float8 byte
2 The first sub-pixel coordinate pair stored is for the feature at cell-coordinate (1,0). float, float 8 bytes
3 The first sub-pixel coordinate pair stored is for the feature at cell-coordinate (2,0).float, float 8 bytes
4 ...