6,551 research outputs found
A statistical normalization method and differential expression analysis for RNA-seq data between different species
Background: High-throughput techniques bring novel tools but also statistical
challenges to genomic research. Identifying genes with differential expression
between different species is an effective way to discover evolutionarily
conserved transcriptional responses. To remove systematic variation between
different species for a fair comparison, the normalization procedure serves as
a crucial pre-processing step that adjusts for the varying sample sequencing
depths and other confounding technical effects.
Results: In this paper, we propose a scale based normalization (SCBN) method
by taking into account the available knowledge of conserved orthologous genes
and hypothesis testing framework. Considering the different gene lengths and
unmapped genes between different species, we formulate the problem from the
perspective of hypothesis testing and search for the optimal scaling factor
that minimizes the deviation between the empirical and nominal type I errors.
Conclusions: Simulation studies show that the proposed method performs
significantly better than the existing competitor in a wide range of settings.
An RNA-seq dataset of different species is also analyzed and it coincides with
the conclusion that the proposed method outperforms the existing method. For
practical applications, we have also developed an R package named "SCBN" and
the software is available at
http://www.bioconductor.org/packages/devel/bioc/html/SCBN.html
Information Filtering on Coupled Social Networks
In this paper, based on the coupled social networks (CSN), we propose a
hybrid algorithm to nonlinearly integrate both social and behavior information
of online users. Filtering algorithm based on the coupled social networks,
which considers the effects of both social influence and personalized
preference. Experimental results on two real datasets, \emph{Epinions} and
\emph{Friendfeed}, show that hybrid pattern can not only provide more accurate
recommendations, but also can enlarge the recommendation coverage while
adopting global metric. Further empirical analyses demonstrate that the mutual
reinforcement and rich-club phenomenon can also be found in coupled social
networks where the identical individuals occupy the core position of the online
system. This work may shed some light on the in-depth understanding structure
and function of coupled social networks
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