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The DAT
file contains pixel intensity values collected from an Affymetrix scanner.
The information below will describe the following versions:
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.
The 512 byte header contains the following information:
| Item | Description | Type |
| 1 | Type of file,
must be 0xFC. | BYTE | | 2 | Number
of pixels per line. | WORD | | 3 |
Number of lines in the image. | WORD |
| 4 | The total number
of data points (pixels) in the image. | DWORD |
| 5 | Minimum pixel
value in the image. | DWORD | |
6 | Maximum pixel value in the image. | DWORD |
| 7 | Mean pixel
value. | double | |
8 | Standard deviation of the pixel values | double |
| 9 | Number of
pixels per row (padded with spaces), preceded with "CLS=". | char[9] |
| 10 | Number of
rows in the image (padded with spaces), preceded with "RWS=". | char[9] |
| 11 | Pixel width
in micrometers (padded with spaces), preceded with "XIN=" | char[7] |
| 12 | Pixel height
in micrometers (padded with spaces), preceded with "YIN=". | char[7] |
| 13 | Scan 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] |
| 15 | Laser power
in milliwatts or microwatts (padded with spaces. | char[4] |
| 16 | Date 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).
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.
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 |
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