Term

Definition

.astar Files

The file extension for projects created in ArrayStar version 2.1 or later.

.call Files

A NimbleGen™ file type containing microarray data for single or multiple chips.

.cdf Files

An Affymetrix® file type, known as a “chip description” file. These files contain the layout information for a given chip type, such as the number and type of quality control probes and the position of each probe. There is only one .cdf file per chip type.

.cel Files

An Affymetrix® file type that contains the raw intensity values for one chip.

.chp Files

An Affymetrix® file type that contains the results of a probe set analysis on the values in a .cel file.

.dmaproj Files

The file extension for an ArrayStar 2.0 project.

.pair Files

A NimbleGen™ file type containing probe level data.

.psi Files

An Affymetrix® file type, known as a “probe set information” file. These files contain the number of probe pairs and the probe IDs for a given chip type. There is only one .psi file per chip type.

Best-fit line

Also known as the “regression line,” this is a line that passes as near to as many data points as possible on the Scatter Plot.

Biological Replicates

Nucleic acid samples isolated from independent cultures grown under the same condition and hybridized to separate arrays, thus controlling for natural variation and sample preparation.

Distance Metric

In ArrayStar, a calculation of distance used in clustering.

Experiment Tree

The tree drawn above the heat map display that shows the clustering of experiments as calculated by the selected clustering method.

Gene Set

A saved collection of genes that you can name, annotate, and export.

Gene Tree

The tree drawn to the left of the heat map display that shows the clustering of genes as calculated by the selected clustering method.

Linkage Method

In ArrayStar, a method used in Hierarchical Clustering to define how data points are clustered based on the distance between them.

Multiple Testing Correction

A method used to adjust the p-values in a probabilistic statistical test with the objective of reducing the number of false positives.

Replicate Set

A group of experiments, defined in the Experiment List view, that will be averaged and treated as a single experiment within ArrayStar.

Technical Replicates

A nucleic acid sample isolated from a single culture and hybridized to multiple arrays, thus controlling for variability in factors such as array manufacturing, hybridization efficiency, and processing.