Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Differential protein expression and peak selection in mass spectrometry
  data by binary discriminant analysis   Motivation: Proteomic mass spectrometry analysis is becoming routine in
clinical diagnostics, for example to monitor cancer biomarkers using blood
samples. However, differential proteomics and identification of peaks relevant
for class separation remains challenging.
  Results: Here, we introduce a simple yet effective approach for identifying
differentially expressed proteins using binary discriminant analysis. This
approach works by data-adaptive thresholding of protein expression values and
subsequent ranking of the dichotomized features using a relative entropy
measure. Our framework may be viewed as a generalization of the `peak
probability contrast' approach of Tibshirani et al. (2004) and can be applied
both in the two-group and the multi-group setting.
  Our approach is computationally inexpensive and shows in the analysis of a
large-scale drug discovery test data set equivalent prediction accuracy as a
random forest. Furthermore, we were able to identify in the analysis of mass
spectrometry data from a pancreas cancer study biological relevant and
statistically predictive marker peaks unrecognized in the original study.
  Availability: The methodology for binary discriminant analysis is implemented
in the R package binda, which is freely available under the GNU General Public
License (version 3 or later) from CRAN at URL
http://cran.r-project.org/web/packages/binda/ . R scripts reproducing all
described analyzes are available from the web page
http://strimmerlab.org/software/binda/ .

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The categories of this paper are: alg-geom
3
The categories of this paper are: physics
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The categories of this paper are: bayes-an
7
The categories of this paper are: hep-th
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The categories of this paper are: mtrl-th
6
The categories of this paper are: astro-ph
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The categories of this paper are: chem-ph
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The categories of this paper are: q-fin
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The categories of this paper are: eess
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The categories of this paper are: solv-int
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The categories of this paper are: comp-gas
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The categories of this paper are: funct-an
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The categories of this paper are: econ
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The categories of this paper are: chao-dyn
2
The categories of this paper are: math
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The categories of this paper are: cs