Affymetrix® BAR Data File Format

BAR FILE

Description

The BAR file contains one and two sample analysis results (signal and p-values) from the tiling array software.

Format

The format of the BAR file is a binary file with data stored in big-endian format. The format of the file is a header section followed by sequences sections (one section per sequence defined).

Section Definitions

File Header

Item DescriptionType Size
1 Magic number. A value to identify the file type. The value is set to "barr\r\n\032\n. char8 bytes
2 The version number of the file. The version number is either 1.0 or 2.0. float 4 bytes
3 Number of sequences stored in the file. This will be referred to as NSEQ. integer 4 bytes
4 Number of columns per data point. This will be referred to as NCOL. integer 4 bytes
5 The field types, one per column of data. The possible values are:

0 – Double
1 – Float
2 – 4 byte signed integer
3 – 2 byte signed integer
4 – 1 byte signed integer
5 – 4 byte unsigned integer
6 – 2 byte unsigned integer
7 – 1 byte unsigned integer

Currently only types 1 and 2 are used in Affymetrix BAR files.

integer 4*NCOL
6 The number of parameter name/value pairs. The parameter names and values are stored as strings.

Note: Items 7-10 are repeated for each parameter.

integer 4 bytes
7 The length of the parameter name.integer 4 bytes
8 The parameter name.char Specified by item #7.
9 The length of the parameter value.integer 4 bytes
10 The parameter value.char Specified by item #9.

Sequence

Item DescriptionType Size
1 The length of the sequence name. Referred to as SEQNAMELEN. integer4 bytes
2 The sequence name. charSpecified by item #1
3 The length of the sequence group name. (only for version 2.0 and above files). integer4 bytes
4 The name of the group which the sequence is a member (for example, often specifies organism). (only for version 2.0 and above files). char Specified by item #3
5 The length of the sequence version.integer 4 bytes
6 The sequence version.char Specified by item #5
7 The number of parameter name/value pairs. (only for version 2.0 and above files).

Note: Items 8-11 are repeated for each parameter.

integer 4 bytes
8 The length of the parameter name. (only for version 2.0 and above files). integer 4 bytes
9 The name of the parameter. (only for version 2.0 and above files). char Specified by item #8
10 The length of the parameter value. (only for version 2.0 and above files). integer 4 bytes
11 The value of the parameter. (only for version 2.0 and above files). char Specified by item #10
12 The number of data points defined in the sequence. Each data point will contain NCOL column values.integer 4 bytes
13 The next set of values in the file is the data points for the sequence. Each data point contains NCOL column values. The type, thus the size, of each column is defined above in the field types section. see description. see description.