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Minor rewording to abstract, fixed funding number.
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Aaron Lun committed Aug 20, 2018
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\section*{Abstract}
Applying a log-transformation to normalized data is one of the most common procedures in exploratory analyses of single-cell RNA sequencing (scRNA-seq) data.
Normalization removes systematic biases in sequencing coverage between cells, while the log-transformation ensures that algorithms operate on relative rather than absolute differences in expression.
Applying a log-transformation to normalized expression values is one of the most common procedures in exploratory analyses of single-cell RNA sequencing (scRNA-seq) data.
Normalization removes systematic biases in sequencing coverage between cells, while the log-transformation ensures that downstream computational procedures operate on relative rather than absolute differences in expression.
We show that the log-transformation can introduce systematic errors when cells vary in sequencing coverage,
leading to spurious non-zero differences in expression and artificial population structure in simulations.
We observe similar effects in real scRNA-seq data where the difference in transformed values between groups of cells is not an accurate proxy for the log-fold change.
We provide some practical recommendations to overcome this effect and derive an expression for a larger pseudo-count that controls the transformation-induced error to a specified threshold.
We provide some practical recommendations to overcome this effect and analytically derive an expression for a larger pseudo-count that controls the transformation-induced error to a specified threshold.

\section{Background}
Log-transformed expression values are widely used in exploratory analyses of single-cell RNA sequencing (scRNA-seq) data.
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\section{Acknowledgements}
We would like to thank Dr.\ John Marioni for helpful suggestions on the manuscript.
This work was supported by core funding from Cancer Research UK (award no. 17197 to Dr.\ Marioni).
This work was supported by core funding from Cancer Research UK (award no. A17197 to Dr.\ Marioni).

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