Affymetrix® DAT Data File Format

DAT FILE

Description

The DAT file contains pixel intensity values collected from an Affymetrix scanner.

The information below will describe the following versions:

Version 1 Format

The file is a binary file with a 512 byte header followed by 16 bit unsigned integer pixel intensity values. Values are stored in little-endian format.

Header

The 512 byte header contains the following information:

ItemDescriptionType
1Type of file, must be 0xFC.BYTE
2Number of pixels per line.WORD
3 Number of lines in the image.WORD
4The total number of data points (pixels) in the image.DWORD
5Minimum pixel value in the image. DWORD
6 Maximum pixel value in the image.DWORD
7Mean pixel value. double
8 Standard deviation of the pixel valuesdouble
9Number of pixels per row (padded with spaces), preceded with "CLS=".char[9]
10Number of rows in the image (padded with spaces), preceded with "RWS=".char[9]
11Pixel width in micrometers (padded with spaces), preceded with "XIN="char[7]
12Pixel height in micrometers (padded with spaces), preceded with "YIN=".char[7]
13Scan speed in millimeters per second (padded with spaces), preceded with "VE=". char[6]
14 Temperature in degrees Celsius (padded with spaces). If no temperature was set then the entire field is empty.char[7]
15Laser power in milliwatts or microwatts (padded with spaces.char[4]
16Date and time of scan (padded with spaces). char[18]
17

There are several sub-fields in this field. The first sub field is the scanner ID, sometimes  followed by a number, followed by three spaces. If the scanner ID is absent, the field consists of four spaces.

Next are 10 structured comment fields. Each field is preceded by the delimiter 0x14 and a space. The field is followed by a space and 0x14. Only field two is valid, the other 9 fields are obsolete. Field 2 contains the probe array type, followed by .1sq. The 1sq extension is also obsolete.

Next (after the last structured field) there is the chip orientation preceded by a space.

The rest of the field is filled with nulls (zeros)

char[220]
18 Average DC Offset of the scanner for this image. double
19 Standard deviation of the average DC offset. double
20 Number of samples taken in determining the DC offset. DWORD
21 Coordinates of the grid's upper left corner. POINTS
22 Coordinates of the grid's upper right corner. POINTS
23 Coordinates of the grid's lower right corner. POINTS
24 Coordinates of the grid's lower left corner. POINTS
25 Cell margin used for computing the cells intensity value. WORD
26 Name of the experiment padded with nulls. char[154]

Types used are defined as: BYTE (An 8-bit unsigned integer), SHORT (A 16-bit integer), WORD (A 16-bit unsigned integer), DWORD (A 32-bit unsigned integer), double (An 64-bit floating-point number), char (8-bit character) and POINTS (A structure that defines coordinates of a point. The contents of the structure are two SHORT values describing the X and Y values of the coordinate).

Data

The pixel intensity data is stored following the header at byte 512. Intensity values are stored as 16 bit unsigned integer values. Data is stored by rows.

Command Console Format

The format of the DAT file generated by the Command Console software uses the Command Console generic data format. The following describes the data sets and groups in the file.

The generic data header shall include:

The data type identifier is set to "affymetrix-calvin-scan-acquisition"

The parameters stored in the file include:

Parameter Name Definition
affymetrix-array-type The probe array type.
affymetrix-pixel-size The pixel size.
affymetrix-scanner-type The scanner type. e.g. M10 for the GCS3000 high resolution scanner.
affymetrix-scanner-id The scanner ID
affymetrix-scan-date The date of the scan.
affymetrix-pixel-rows The number of rows of pixels.
affymetrix-pixel-cols The number of columns of pixels.
affymetrix-partial-dat-header DAT header string without min and max intensity. Present if this is a native Command Console DAT file.
affyemtrix-max-pixel-intensity Max pixel intensity.  Present if this is a native Command Console DAT file.
affymetrix-min-pixel-intensity Min pixel intensity. Present if this is a native Command Console DAT file.
affymetrix-full-dat-header Full DAT header string.  Present if this is a DAT file converted from GCOS.
affymetrix-image-orientation A code indicating the orientation of the image.
affymetrix-file-version File version.
affymetrix-image-flip-flag Indicates if the image has been flipped about the y-axis.

Array file parameters (if available) will be stored within the parent data header object. Parameters include:

Parameter Name Definition
affymetrix-array-id A GUID that identifies the array.
affymetrix-array-barcode The array barcode.

The data is stored in a single group with 4 data sets. The data sets are defined as:

Data Set Name Description Number of Columns Column Name Column Type Description
Pixel The intensity values for each pixel. 1 Pixel USHORT The pixel intensities.
Stats The minimum and maximum pixel value. 2 Min Intensity
Max Intensity
USHORT
USHORT
The minimum pixel value.
The maximum pixel value.
GlobalGrid The status of the grid and the 4 corners that define the global grid. 9

GridStatus

Upper left x
Upper left y

Upper right x
Upper right y

Lower right x
Lower right y

Lower left x
Lower left y

UINT

FLOAT
FLOAT

FLOAT
FLOAT

FLOAT
FLOAT

FLOAT
FLOAT

The status of the grid. OK=1, Error=2, Manual Adjust=4

The X coordinate of the upper left corner
The Y coordinate of the upper left corner

The X coordinate of the upper right corner
The Y coordinate of the upper right corner

The X coordinate of the lower right corner
The Y coordinate of the lower right corner

The X coordinate of the lower left corner
The Y coordinate of the lower left corner

Subgrid The status of the grid and the 4 corners that define each sub-grid. 9

GridStatus

Upper left x
Upper left y

Upper right x
Upper right y

Lower right x
Lower right y

Lower left x
Lower left y

UINT

FLOAT
FLOAT

FLOAT
FLOAT

FLOAT
FLOAT

FLOAT
FLOAT

The status of the grid. OK=1, Error=2, Manual Adjust=4

The X coordinate of the upper left corner
The Y coordinate of the upper left corner

The X coordinate of the upper right corner
The Y coordinate of the upper right corner

The X coordinate of the lower right corner
The Y coordinate of the lower right corner

The X coordinate of the lower left corner
The Y coordinate of the lower left corner