Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: GaGa: A parsimonious and flexible model for differential expression
  analysis   Hierarchical models are a powerful tool for high-throughput data with a small
to moderate number of replicates, as they allow sharing information across
units of information, for example, genes. We propose two such models and show
its increased sensitivity in microarray differential expression applications.
We build on the gamma--gamma hierarchical model introduced by Kendziorski et
al. [Statist. Med. 22 (2003) 3899--3914] and Newton et al. [Biostatistics 5
(2004) 155--176], by addressing important limitations that may have hampered
its performance and its more widespread use. The models parsimoniously describe
the expression of thousands of genes with a small number of hyper-parameters.
This makes them easy to interpret and analytically tractable. The first model
is a simple extension that improves the fit substantially with almost no
increase in complexity. We propose a second extension that uses a mixture of
gamma distributions to further improve the fit, at the expense of increased
computational burden. We derive several approximations that significantly
reduce the computational cost. We find that our models outperform the original
formulation of the model, as well as some other popular methods for
differential expression analysis. The improved performance is specially
noticeable for the small sample sizes commonly encountered in high-throughput
experiments. Our methods are implemented in the freely available Bioconductor
gaga package.

7
The categories of this paper are: hep-th
0
The categories of this paper are: hep-ph
22
The categories of this paper are: chao-dyn
31
The categories of this paper are: ao-sci
20
The categories of this paper are: acc-phys
25
The categories of this paper are: patt-sol
18
The categories of this paper are: econ
21
The categories of this paper are: adap-org
24
The categories of this paper are: dg-ga
30
The categories of this paper are: q-alg
32
The categories of this paper are: atom-ph
35
The categories of this paper are: mtrl-th
3
The categories of this paper are: physics
15
The categories of this paper are: nucl-ex
36
The categories of this paper are: cmp-lg
11
The categories of this paper are: hep-lat