Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Removing System Noise from Comparative Genomic Hybridization Data by
  Self-Self Analysis   Genomic copy number variation (CNV) is a large source of variation between
organisms, and its consequences include phenotypic differences and genetic
disorders. CNVs are commonly detected by hybridizing genomic DNA to microarrays
of nucleic acid probes. System noise caused by operational and probe
performance variability complicates the interpretation of these data. To
minimize the distortion of genetic signal by system noise, we have explored the
latter in an archive of hybridizations in which no genetic signal is expected.
This archive is obtained by comparative genomic hybridization (CGH) of a sample
in one channel to the same sample in the other channel, or 'self-self' data.
These self-self hybridizations trap a variety of system noise inherent in
sample-reference (test) data. Through singular value decomposition (SVD) of
self-self data, we have determined the principal components of system noise.
Assuming simple linear models of noise generation, the linear correction of
test data with self-self data -or 'system normalization'- reduces local and
long-range correlations and improves signal-to-noise metrics, yet does not
introduce detectable spurious signal. Using this method, 90% of hybridizations
displayed improved signal-to-noise ratios with an average increase of 7.0%, due
mainly to a reduced median average deviation (MAD). In addition, we have found
that principal component loadings correlate with specific probe variables
including array coordinates, base composition, and proximity to the 5' ends of
genes. The correlation of the principal component loadings with the test data
depends on operational variables, such as the temporal order of processing and
the localization of individual samples within 96-well plates.

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The categories of this paper are: atom-ph
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The categories of this paper are: ao-sci
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The categories of this paper are: bayes-an
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The categories of this paper are: econ
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The categories of this paper are: math-ph
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The categories of this paper are: hep-lat
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The categories of this paper are: plasm-ph
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The categories of this paper are: astro-ph
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The categories of this paper are: cond-mat
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The categories of this paper are: supr-con
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The categories of this paper are: hep-ph
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The categories of this paper are: comp-gas
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The categories of this paper are: hep-th
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The categories of this paper are: chem-ph
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The categories of this paper are: chao-dyn
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The categories of this paper are: q-alg