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This is because Raw only counts the number of common aberrations in computing the similarity between two samples (if both the values are 0, they are not counted).
Genes should not be called DE between two samples if they are closer in expression than the resolution of the technology.
A gene was considered to be differentially expressed between two samples if the corrected p-value (FDR) ≤ 0.001 and the fold change ≥ 2.
The coefficient of distance which was used - shared allele distance - takes into consideration the proportion of alleles shared between two samples: if two individuals share 6 alleles out of a total of 10 allele copies, the coefficient of distance between them is 1 - (6/10) = 0.4.
Similar(56)
Within each run, voxels were eliminated if the signal magnitude changed more than 30% between two samples or if the mean signal level was below a threshold defined by the noise inherent in the data.
Differences between two samples were tested with paired, two-tailed Student's t-tests.
If differences were found to be significant, the Mann–Whitney U-test was applied to compare differences between two samples.
Distinguishing if a given gene expression intensity value is greater than the background noise or is different between two samples are fundamental issues in microarray analysis.
A central problem with this analysis is that the statistical test does not account for the two tiers of sampling noted earlier, and at increasingly higher levels of coverage, the authors would have concluded that more and more SNP frequencies differed significantly between the two samples even if they were invariant in the actual populations.
If homogeneity between the two samples was confirmed, then the classification was considered validated, and OR (95% CI) were estimated by conditional logistic regression on the entire sample (samples A and B combined).
If the variance between the two samples was greater than the previously observed maximum uncertainty (15%), a third sample was measured and the average was calculated.
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CEO of Professional Science Editing for Scientists @ prosciediting.com