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These data manipulations were necessary because the oligo-nucleotide array data was collected as the intensity ratio between the experimental sample and a common reference, while the photolithography data was collected as the total signal intensity at each spot.
CLASP assigns each match a PIA that is simply the maximum PIA for that sample compared to all the other samples in H: For each match result, CLASP also returns an alignment score, which is simply the percent haplotype identity between the experimental sample and the closest matching reference sample.
Similar(58)
To determine the contribution of individual genera to the average Bray-Curtis dissimilarity between the experimental samples and the reference samples, the similarity percentages analysis (SIMPER) was applied to nematode relative abundances.
To examine the relationship between the experimental samples, Pearson correlation coefficient (PCC) analysis was performed on these genes obtained from all 24 libraries.
The results showed that the morphology and the growth of the precipitated layer (remineralized layer) was different between the experimental samples (with the oligopeptide) and the control samples (without oligopeptide).
The first normalization was completed using actin internal reference to get a ∆Ct value (Cttarget − Ctactin), and then the second was done by the comparison between ∆Ct value of the experimental sample and that of the control sample (∆∆Ct = ∆Cttarget − ∆Ctcontrol).
This suggests that the technical variation is not the same between the spike-ins and the experimental sample.
Comparison analysis defines a gene as up-regulated if the signal log ratio between the baseline sample and the experimental sample is larger than 1 (2-fold) and the experimental sample is present.
We note that there are differences between our experiment and that of [ 8] that might have contributed to the differences in technical variation between the spike-ins and the experimental sample in our data.
In addition, corrections can readily be made to allow for difference in crystallinity between the control and the experimental samples.
The appropriate dilution of the test Ab was determined from a previous Ab titration of its binding to gp120 and was chosen to give absorbance reading between 1 and 2. The experimental samples were done in duplicate and the test antibody control (without the competing Abs) was done in quadruplicates.
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