Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Random-set methods identify distinct aspects of the enrichment signal in
  gene-set analysis   A prespecified set of genes may be enriched, to varying degrees, for genes
that have altered expression levels relative to two or more states of a cell.
Knowing the enrichment of gene sets defined by functional categories, such as
gene ontology (GO) annotations, is valuable for analyzing the biological
signals in microarray expression data. A common approach to measuring
enrichment is by cross-classifying genes according to membership in a
functional category and membership on a selected list of significantly altered
genes. A small Fisher's exact test $p$-value, for example, in this $2\times2$
table is indicative of enrichment. Other category analysis methods retain the
quantitative gene-level scores and measure significance by referring a
category-level statistic to a permutation distribution associated with the
original differential expression problem. We describe a class of random-set
scoring methods that measure distinct components of the enrichment signal. The
class includes Fisher's test based on selected genes and also tests that
average gene-level evidence across the category. Averaging and selection
methods are compared empirically using Affymetrix data on expression in
nasopharyngeal cancer tissue, and theoretically using a location model of
differential expression. We find that each method has a domain of superiority
in the state space of enrichment problems, and that both methods have benefits
in practice. Our analysis also addresses two problems related to
multiple-category inference, namely, that equally enriched categories are not
detected with equal probability if they are of different sizes, and also that
there is dependence among category statistics owing to shared genes. Random-set
enrichment calculations do not require Monte Carlo for implementation. They are
made available in the R package allez.

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The categories of this paper are: alg-geom
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The categories of this paper are: quant-ph
35
The categories of this paper are: mtrl-th
1
The categories of this paper are: cs
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The categories of this paper are: q-fin
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The categories of this paper are: chao-dyn
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The categories of this paper are: hep-ex
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The categories of this paper are: cmp-lg
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The categories of this paper are: supr-con
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The categories of this paper are: adap-org
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The categories of this paper are: atom-ph
10
The categories of this paper are: q-bio
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The categories of this paper are: chem-ph
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The categories of this paper are: funct-an
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The categories of this paper are: solv-int
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The categories of this paper are: nucl-th