Calculate Statistics

In ArrayStar, the following statistical analyses can be accessed via the Statistics menu to aid in identifying differentially expressed genes:

•      Fisher's Exact Test Signal Search

•      Fisher's Exact Test SNP Search (Variants workflow only)

•      Odds Ratio SNP Search (Variants workflow only)

•      Standard Deviation (see ArrayStar Menu Commands, Statistics section)

•      Coefficient of Variation (see ArrayStar Menu Commands, Statistics section)

•      Variance (see ArrayStar Menu Commands, Statistics section)

•      Cross-R²

•      Validation Control Accuracy

•      Student's t-Test

•      Moderated t-Test

•      F-Test (ANOVA)

Selecting any of these options from the Statistics menu will launch the Statistics Parameters dialog. This dialog allows you to define the data (e.g., replicate sets) to be included in the analysis, as well as the Multiple Testing Correction adjustment to be used. After clicking Calculate, calculations are made for each gene and the results added to the Gene Table.

Notes regarding statistical test results:

•      In general, if the resulting T/F value is large, then the assumption can be made that the gene is differentially expressed. The P-value represents the probability that the calculated T/F value occurred by chance. In general, the lower the P-value, the more confidence there is that the gene is differentially expressed.

•      After performing a statistical test, some tables may contain the abbreviation "NaN" ("Not a Number"). This abbreviation denotes that the value could not be calculated. In ArrayStar, this is generally due to one of the following:

o  There is only one valid replicate value.

o  There is no variance between multiple replicates.

o  The value cannot be calculated from a negative number; this can occur with statistics using log-values.