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Hence, the constant factor in the tanh normalization was set to 0.1 [138]38]).
Normalization was set up according to the total spot density.
b i, which describes the need for normalization, was set to be zero.
Effective gene length in TPM normalization was set to be g e n e _ l e n g t h + r e a d _ l e n g t h − 1 to account for reads that extend beyond annotated gene models.
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The parameter α of the power normalization is set to 0.5 as reported in [46].
Thresholds for CN alterations after normalization were set at 0.92 for losses and 1.08 for gains, compared to the sample mean.
Raw expression values <0.01 were set to 0.01 and the normalization per chip was set to the 50th percentile.
The raw signals were log transformed and normalized using the Percentile shift normalization method, the value was set at 75th percentile.
The probe intensities were normalized using quantile normalization plus scaling, and bandwidth was set at 250 bp.
For all normalizations, the smoothing parameter was set to 0.33.
After normalization, the wild-type sample was set to a value of 1 and each mutant expressed relative to wild-type with statistical significance determined by Student's t test.
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CEO of Professional Science Editing for Scientists @ prosciediting.com