Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Modelling background intensity in Affymetrix Genechips   DNA microarrays are devices that are able, in principle, to detect and
quantify the presence of specific nucleic acid sequences in complex biological
mixtures. The measurement consists in detecting fluorescence signals from
several spots on the microarray surface onto which different probe sequences
are grafted. One of the problems of the data analysis is that the signal
contains a noisy background component due to non-specific binding. This paper
presents a physical model for background estimation in Affymetrix Genechips. It
combines two different approaches. The first is based on the sequence
composition, specifically its sequence dependent hybridization affinity. The
second is based on the strong correlation of intensities from locations which
are the physical neighbors of a specific spot on the chip. Both effects are
incorporated in a background functional which contains 24 free parameters,
fixed by minimization on a training data set. In all data analyzed the sequence
specific parameters, obtained by minimization, are found to strongly correlate
with empirically determined stacking free energies for RNA/DNA hybridization in
solution. Moreover, there is an overall agreement with experimental background
data and we show that the physics-based model proposed in this paper performs
on average better than purely statistical approaches for background
calculations. The model thus provides an interesting alternative method for
background subtraction schemes in Affymetrix Genechips.

14
The categories of this paper are: math-ph
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The categories of this paper are: q-fin
16
The categories of this paper are: stat
20
The categories of this paper are: acc-phys
23
The categories of this paper are: solv-int
34
The categories of this paper are: chem-ph
22
The categories of this paper are: chao-dyn
5
The categories of this paper are: gr-qc
0
The categories of this paper are: hep-ph
27
The categories of this paper are: comp-gas
33
The categories of this paper are: plasm-ph
26
The categories of this paper are: bayes-an
37
The categories of this paper are: supr-con
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The categories of this paper are: cmp-lg
18
The categories of this paper are: econ
31
The categories of this paper are: ao-sci