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Between 103 and 107 copies, there was no evidence of cross-reactivity for any of the Prevotella qPCR assays with a mean amount of target bacteria detected of 91% (range, 73 113%) of the expected copy number.
After normalisation, negative ΔCt values were assigned to zero to reflect their expected copy number state.
"Copy nr E": expected copy number of the region counted by y = kx+B formula (*- exceptions, where the expected copy number was different from the real copy number due to heterogeneity or few data points).
Results were assembled into groups of 100 by expected copy number and 600 were examined by a manual editor.
Among the four CNVRs selected for validation through qPCR, all four variations exhibited the expected copy number differences.
Expected copy number can thus be calculated from the coverage of each sequence window across the alignment.
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Expected copy numbers were obtained (Figure 2).
This tendency was reversed for expected copy numbers of 79 or lower [ 9].
Deviations from Poisson distribution were tested using chi-square goodness of fit, pooling adjacent classes with low expected copy numbers.
Expected copy numbers in BLG2 and MSM were calculated from the average of the aCGH values and the copy number in B6 (Additional file 7).
c Expected copy numbers in B6 were calculated from the number of homologous sequences in each of the 60 groups (Additional file 5).
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