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In total, 87 (2%) genes from RNA-seq and 64 (1.5%) from microarray qualified at this cut-off threshold from the 4312 consensus genes (Additional file 1: Table S4).
We counted for the number of known hrp cluster genes, which passed the FC and FDR cut-off thresholds from RNA-seq and microarray methods (Table 1).
Adjusting the cut-off threshold for generating the binary masks from the CNN's probability output can be used to increase the sensitivity of the method.
Consequently, reducing the cut-off threshold for anti-CCP titer to 2 U/ml improved the sensitivity for predicting erosions from 53% to 59%.
The first strategy employs a cut-off threshold derived from a separate characterized strain or other published results [ 32, 33].
If the values of any atoms in the ligand were less than the cut-off threshold value from the point, the prediction was assumed to be correct.
From the derived relationship, increasing the subgroup size in ECOMF is equivalent to decreasing the cut-off threshold in ECOMP.
A cut-off threshold of 0.5 has been used to decide on the number of principal components to retain from the data set.
A range of −2 to 2 was chosen (i.e. 5 cut-off thresholds ranging from 7 to 11).
This minimum was selected by traveling through the Ncut cost landscape in descending direction of the number of clusters starting with 50 (i.e. from 50 to 2) -partitioning the data in as much meaningful networks as possible- and in ascending direction of the cut-off threshold (i.e up from 2 to 25), keeping the information in Ggrp as high as possible.
Since we wanted to assess reproducibility of positive tumor with respect to the 10% cut-off threshold, we selected cases from the previous study that had been problematic in whether the positive tumor ratio was above or below 10%, and added some cases with a positive tumor ratio in higher ranges.
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