The first line gives the column headings. Each subsequent line contains the (X,Y) intensity pairs for a particular gene. Alternatively, lines after the first line that begin with a '#' are skipped (used for comments).
An example data file containing 2 genes and up to 3 replicates:
unique other X0 Y0 X1 Y1 X2 Y2 N F0 F1 F2 # # optional comments appear here... # b01 actin 12 30 5 6 24 60 3 - - X c35 unknown 100 21 10 3 - - 2 - X -
|-----------------required------------------||----optional---| |-order fixed--||--------------------order arbitrary---------|
The first two columns contain text descriptors for each gene: the first must uniquely identify the gene (e.g. a gene name or ORF code), while the second column is used to store additional information about the gene and is allowed to be nonunique. The corresponding column headings "unique" and "other" may be chosen at will.
Also required are the replicate (X,Y) intensity pairs for each gene. The headings for these columns must be labeled as shown above (X or Y followed by the repeat number, starting from repeat 0), although column order does not matter.
Optional columns:The N column specifies the number of replicates to be used (replicates 0 through N-1). The F (flag) columns specify which specific pairs are to be excluded (see "Data handling" below). The headings for these columns must be labeled as shown above (N; or F followed by the repeat number).
Data handling:| N | F | Handling |
| not given | not given | Pairs are excluded only if '-' place holder found in either X or Y. |
| not given | given | Pairs are excluded if an 'X' is found in the flag entry, or if the a '-' place holder is found in either X or Y. In the above example, only the (X0,Y0) and (X1,Y1) pairs will be used for actin. |
| given | not given | The first N pairs are used. For the unknown gene above, only the pairs (X0,Y0) and (X1,Y1) are used. |
| given | given | F flag overrides number of samples N. |