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Minor typo fixes.
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Aaron Lun committed Aug 28, 2018
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2 changes: 1 addition & 1 deletion report/main.tex
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Expand Up @@ -454,7 +454,7 @@ \section{Practical use of larger pseudo-counts}
Methods like TREAT \cite{mccarthy2009testing} can also be applied to test whether the observed log-difference is significantly greater than the theoretical limit $\tau$.
This provides a statistically rigorous alternative for DE analyses if count-based models are impractical.
It is also possible to use log-values computed with $\hat c$ in the initial exploratory analysis, which may reduce the risk of detecting spurious structures in the first place.
However, this is more difficult to justify as there is no straightforward interpretion for an ``acceptable'' threshold in the error in the distance between cells.
However, this is more difficult to justify as there is no straightforward interpretation for an ``acceptable'' threshold in the error in the distance between cells.

Pseudo-counts are often set to unity for practical reasons that have little to do with avoiding spurious differences.
One reason is to ensure that zero counts always yield zero log-values, which ensures that sparse matrix representations are still effective for reducing memory usage when analyzing large data sets.
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2 changes: 1 addition & 1 deletion report/ref.bib
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Expand Up @@ -259,7 +259,7 @@ @article{ohara2010do
}

@Article{huber2015orchestrating,
Author="Huber, W. and Carey, V. J. and Gentleman, R. and Anders, S. and Carlson, M. and Carvalho, B. S. and Bravo, H. C. and Davis, S. and Gatto, L. and Girke, T. and Gottardo, R. and Hahne, F. and Hansen, K. D. and Irizarry, R. A. and Lawrence, M. and Love, M. I. and MacDonald, J. and Obenchain, V. and Ole?, A. K. and Pages, H. and Reyes, A. and Shannon, P. and Smyth, G. K. and Tenenbaum, D. and Waldron, L. and Morgan, M. ",
Author="Huber, W. and Carey, V. J. and Gentleman, R. and Anders, S. and Carlson, M. and Carvalho, B. S. and Bravo, H. C. and Davis, S. and Gatto, L. and Girke, T. and Gottardo, R. and Hahne, F. and Hansen, K. D. and Irizarry, R. A. and Lawrence, M. and Love, M. I. and MacDonald, J. and Obenchain, V. and Ole\'s, A. K. and Pages, H. and Reyes, A. and Shannon, P. and Smyth, G. K. and Tenenbaum, D. and Waldron, L. and Morgan, M. ",
Title="{{O}rchestrating high-throughput genomic analysis with {B}ioconductor}",
Journal="Nat. Methods",
Year="2015",
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