Task: Class Definition Understanding (ontology: Sciences/Computer_Science)

Which of the following definitions best describes 'SPIA'?

A. the concept approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values.
B. A variety of data files and functions for the analysis of genetic interactions
C. This package implements the Signaling Pathway Impact Analysis (the concept) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.
D. EBarrays provides tools for the analysis of replicated/unreplicated microarray data.

Answer: This package implements the Signaling Pathway Impact Analysis (the concept) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.