Data files

To use the program, place your data into three files. The file names must have extensions .row, .col and .dat, and a common base name. For example, they could be called: MyData.row, MyData.col, and MyData.dat. The contents of these files are described below. When the program starts, it will give the prompt:

Enter data set name:

The user then types MyData at the prompt and presses Enter. A given folder can contain many .row, .col and .dat triples of files.

The file MyData.row should contain the names of the genes to be analyzed. There should be one gene per line of input. The gene names can contain spaces or tabs. A gene name can contain up to $999$ characters.

The file MyData.col should contain the names of the samples. There should be one sample line per line of input and the sample names can be up to $999$ characters long.

The gene and sample names are used to label output. The program does not do any computation with them. In particular it is possible for two or more of the gene (or sample) names to be identical. Before using these names, Plaid replaces spaces and tabs contained within the names with underscore _ characters. Thus ``Mouse liver'' is changed to ``Mouse_liver''. This makes it easier for other programs to read through the Plaid output. These changes are not written out to the .row and .col files.

The Plaid program counts the number of names in files MyData.row and MyData.col. Suppose that there are $n$ row names and $p$ column names. Then the file MyData.dat should contain an $n$ by $p$ matrix of data values. There must be exactly $n$ rows of data in this file, one row per line. Each row must contain exactly $p$ numbers. Missing values are not allowed. They can be handled as described below. The numbers within a row should be separated by spaces or tabs (not commas).

The Plaid executable, or a shortcut to it, should be present in the same folder that the files are in.