The pcl format is a tab-delimited pre-clustering (pcl) file format developed by the Stanford Microarray Database (SMD: http://genome-www5.stanford.edu/). Note that the pcl file may be saved with the extenion .pcl or .txt.  The following pcl file description was obtained from SMD.

The first three columns in the pcl file are as follows:

* Column 1 (Name): This column contains a name for the entity in that row, such as a yeast ORF systematic name or CLONEID. The column itself can be labelled anything, but by convention it is named YORF when it contains yeast ORF names, CLID when it contains cloneids, and LUID when it contains Locally Unique Identifiers. This column must contain some text on every row.

* Column 2 (Description): This column can contain descriptive information about the entity, e.g. process or function, or a gene symbol. It can be named anything and can optionally be left blank, but the column itself must be present.

* Column 3 (GWEIGHT): This column gives genes different weights, for example if a gene appears on an array twice, it may be given a weight of 0.5 each.  For the most part the entry for this column is a value of 1 for every gene that appears once on the array.  This column must be present, and each row must have an entry.

In addition the file begins with the following two rows:

* Row 1 (Column headers): This contains the column headers as described above for columns 1, 2 and 3, then contains the experiment names for all of the data columns that exist in the file. Each data column must have a text entry as a name for that column.

* Row 2 (EWEIGHT): This is the EWEIGHT row. The entry in the first column for this row should say EWEIGHT, then for each experiment, there should be an EWEIGHT value. This will usually be 1, but if the same experiment is duplicated twice, these repeats may be given an EWEIGHT of 0.5.

* The Data: The remaining cells in the file contain the actual data, such that the row and column specifies to which gene and which experiment a particular piece of data corresponds. In general the pcl file will contain log-transformed data (typically log2 ratios).