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Concordance was calculated using the initial dataset of 959 significant transcripts (log base 2) with similarity between samples based on Euclidean distance.
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A total of 11,032 EST sequences obtained from isolated immature seeds were used as the initial dataset (178 of them newly described here).
The AMIGA database [ 77] was used to assemble the initial dataset.
As the eServices platform is still in development, synthetic data, based on real data sample and empiric knowledge, is being used to populate the initial dataset.
For the second normalization, print-tip lowess (locally weighted linear regression, Acuity 4.0), an additional percent pixel saturation cutoff and a roundness score were used to filter the initial dataset according to the Acuity manufacturer's recommendations.
The 169 genes (16%) meeting the criteria described above in the datasets generated by all three platforms are tabulated in Additional file 4. The proportions of products detected by commercial antibodies (CAB) and Human Protein Atlas antibodies (HPA) among the 169 Ensembl IDs were the same as those used to generate the initial dataset (38% CAB, 62% HPA).
Table 7 shows the recognition rates obtained using the three classifiers described above for different percentages of the initial dataset reduced using PCA and CA-FR as described in the experimental setup, while Table 8 shows the required training time.
The initial dataset used for interpolation is 30 data points.
The initial dataset used for kriging interpolator is 30 data points.
We trained and respected the ratio between positive (2100) and negative (12,000) samples, as used in [9] at the initial dataset.
Cleveland and collaborators reported the accuracy of the genomic breeding value for the total number of pigs born per litter to be between 0.64 and 0.82, depending on the initial dataset used [ 16].
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