Two designed experiments (latin square and reference sample) that used independent arrays to study the same tissue samples - README

Synteni Data used in ``Analsysis of Variance for Gene Expression Microarrays.''

The data for the ``latin square'' experiment are comprised of red and green fluorescence readings for 1556 spots on array 1 representing 1540 different genes and 1455 spots on array 2 representing 1442 different genes. Spots that are indicated as representing the same gene may not contain the same clones. For each array, gene-identifiers were re-coded to clone identifiers so that each dataset contained as many distinct clone identifiers as spots. For analysis, a combined dataset was created containing readings for clone identifiers appearing for both array 1 and array 2. The final dataset had 1286 clone identifiers representing 1274 different genes.

The ``latin square'' dataset has five columns.
Column 1: Array 1, Liver, Dye 1
Column 2: Array 1, Muscle, Dye 2
Column 3: Array 2, Muscle, Dye 1
Column 4: Array 2, Liver, Dye 2
Column 5: Clone ID
The fluorescence readings in Columns 1-4 are on the natural log scale.

The data for the ``reference design'' experiment are comprised of red and green fluorescence readings for 2125 spots on array 1 representing 2103 different genes and 2098 spots on array 2 representing 2078 different genes. As before, we assigned unique clone identifiers to different spots and created a combined dataset containing clone identifiers appearing on both arrays. The final data set has 1905 clone identifiers representing 1886 different genes.

The ``reference design'' dataset, Synteni.RefDesign.dat, has five columns.
Column 1: Array 1, Placenta, Dye 1
Column 2: Array 1, Liver, Dye 2
Column 3: Array 2, Placenta, Dye 1
Column 4: Array 2, Muscle, Dye 2
Column 5: Clone ID
The fluorescence readings in Columns 1-4 are on the natural log scale.

In both datasets, clones representing the same genes have identifiers that differ after the decimal place; for example, 634.1 and 634.2 are clone identifiers for two different spots representing the same gene.