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The conclusion on MRI and PET/CT may be biased by the low number of datasets.
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ROC curves demonstrated that when testing low numbers of datasets, the accuracy of the DFI ranking only changed slightly between these 100 tests with the area under ROC curve of 0.952 +/- 0.004 (Additional file 3: Figure S3).
For low numbers of input datasets, the fully Bayesian method's loss over existing interactions (L is substantially lower and is the only method to perform better than the naive approach for three input experiments.
To test this hypothesis for the indel dataset, we used only three differential expression categories due to the relatively low number of indels in the dataset: down-regulation, no change, and up-regulation.
All the processing steps were designed taking into account the low number of samples in the dataset, situation that is quite common in medical cases.
The histogram of p-values for miRNAs (Figure 4B) is too noisy to draw any conclusions from it, but this could be partly due to the low number of represented miRNAs in this dataset (130 vs 889 in our brain dataset and 189 in the NCI-60 dataset).
The low number of cell lines in the datasets sensitive to PHA665752 contributed to the difficulty of generating a predictive signature with good precision for this drug.
The consideration of data points instead of substances may further influence the result by a low number of chemicals with an extensive dataset of acute and chronic studies [6].
Because of the low number of CYP3A5 *1/*1 carriers in the dataset (n = 3), these subjects were grouped with CYP3A5 *1/*3 carriers (n = 33) during covariate analysis.
The effect, however, is not as consistent as observed with increasing numbers of regulating miRNA likely due to the relatively low number of repressor genes in this dataset and the fact that not all repressor genes can be expected to exert the same magnitude of regulatory control.
We have not trained HMMs to recognize these groups because of the low number of sequences available from the curated datasets.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com