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It is advisable to obtain the annotation files for your custom chip directly from Affymetrix. If for some reason this is not possible, probe_tab files can be created as a tab-delimited text file using any text editor.
They must contain the following information in columns:

• Probe set nameid
• Probe x position
• Probe y position
• Probe sequence

The first line of the file must be the column headings listed above. Any mixture of upper and lower case is supported. If you are modifying this from another file, the Probe Id column must be the first column in the file. The order of the other columns does not matter and other columns may be present and any additional columns will be ignored unless they are in conflict with the column names above.

The probe set name Probe id can contain any unique identifier but should generally be the Affymetrix probe name or probe set ID. Note that in some chips, such as the Clariom D arrays, the probe id and probe set id contain different information. If that's the case, identify the column containing unique identifiers and use that as your first column. These names have to be composed exclusively of alphanumeric characters, underscores or hyphens.

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• probe set name
• probe name
• probe set id
• probe id
• probe set_name
• probe set_id

In cases where both probe set id and probe id are different, Partek Flow will use the identifier present in the first column. Thus, it it absolutely essential that the first column contains unique identifiers.

The probe position columns must be given for both x and y position.
Valid examples of each are:

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