Exact(4)
Upon further review, four validation datasets were eliminated for reasons outlined in Figure 3.
Only positive correlations above a set cut-off level across all these 10 calculations were used for further analyses; thereby, confounding factors inherent to single datasets were eliminated.
Quantile [ 14] and Lowess [ 15] normalization methods, while widely adopted for gene expression datasets, were eliminated as viable options for ChIP-chip data normalization.
Additionally, datasets were eliminated from the study if BDNF probe sets' expression failed to meet the above mentioned criteria [see Additional file 1: BDNF probe sets].
Similar(56)
Transcript redundancy within the combined datasets was eliminated based on empirically determined criteria, using BLAST [26].
Predicted targets that were not scored as 'Present' in this dataset were eliminated from further analysis.
All datasets of positive and negative sequences (779/779) were subsequently subjected to homology filtering using the CD-HIT clustering algorithm [ 17] where sequences bearing more than 85% sequence identity with any other sequence in the dataset were eliminated.
In addition, duplicates (21) with an existing cassava SSR dataset [ 33] were eliminated.
After positions with gaps and missing data were eliminated a dataset of 1446 positions was retained.
Conformational flexibility and disorder features ('DisorderBinary', 'DisorderReal') were eliminated from dataset one by one and together.
The proteins without CCCH motif were eliminated from the datasets.
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