Exact(1)
However these developments (important as they are) are not yet sufficient to guarantee the reliability of datasets created by a scientific process — the complex activity that scientists carry out in order to create a dataset.
Similar(59)
The reliability of the datasets was assessed by principal components analysis (PCA) (Figure S2) and real-time qRT-PCR of selected genes (Table S3).
These percentages were similar to those previously reported for Bacillus anthracis (94%), Burkholderia mallei (95%) and Sulfolobus solfataricus (89.5%) [23 25], demonstrating the reliability of our datasets.
Bootstrapping was performed 100 times using SEQBOOT[ 96] to obtain support values for each internal branch (to reduce the sampling error, bootstrapping is a method of testing the reliability of a dataset by the creation of pseudo replicate datasets by resampling. Bootstrapping assesses whether stochastic effects have influenced the distribution of amino acids).
Because there were large differences in the number of the gene-pairs and microarrays in the datasets, we sought some measure of the reliability of each dataset.
Since we used a small sample size (30 dogs of each breed) to analyze simulated disease-causative SNPs, one concern is that the power and the reliability of our dataset to detect stratification may be limiting.
Thorough quality control steps are required to ensure the reliability of the dataset.
However, the sample throughput rates are lower for microarrays than for metabolomic analyses so we adopted a different sampling strategy to maximize the reliability of the dataset.
Verification of expression of randomly selected 20 genes in SAM by qRT-PCR, showed a high correlation (R = 0.93) with RNA-seq (in Additional file 2: Table S30), supporting the reliability of our dataset.
The reliability of the dataset was proved by mapping a set of genes and microsatellite markers (11) mapped in the first generation of RH map [ 18] (sequences coming from NCBI) again with new designed primers based on ESTs coming from cDNA libraries produced within the BRIDGEMAP project (see Additional file 2).
In addition to defining a unifying standard, it is critical to use the standard in a manner that accurately reflects the biological reliability of datasets or methods.
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