Crohn's disease status separates with components proportions.

<p>Each marker corresponds to an individual, red for Crohn-free and filled black for Crohn cases. The markers are positioned on the two-dimensional plane defined by the components proportions (there are three components but only two dimensions because the proportions sum to ). The Crohn-free individual at the bottom part of the figure is a colitis case.</p

Increasing the number of samples for a fixed depth of coverage improves both components characterization and binning precision.

<p><b>Left:</b> A fixed number of counts were generated from a model defined by uniformly drawn and matrices using . The value of , the number of samples, varied from 1 to 1000, and 100 trials were performed for each value. The highest average precision of estimation is obtained for . <b>Right:</b> A fixed number of 8,192,000 reads of length 400 bp were sampled from different numbers of samples, each consisting of 15 species in uniformly drawn proportions. The smallest average error over all samples was obtained when 32 samples are sequenced. In both plots the error bars give the standard error of the mean.</p

Association between

<p><b>-mers relative abundances and BMI can be corrected using the components proportions.</b> Quantile-quantile curves comparing the uniform distribution to the distribution of the p-values for association between all -mers and BMI within the Danish samples. The uncorrected p-values are highly deflated (black), indicating that the abundance of many -mers is correlated with BMI. However, when the components proportions are added the the regression equation (red), the correlation disappears for most -mers.</p

Simultaneous binning over multiple samples achieves higher precision compared with the equivalent single-sample approach.

<p>MultiBin and AbundanceBin were both run on datasets of increasing complexity. Each dataset is composed of 5 mixtures of the specified number of species. The specified precision is the proportion of reads correctly assigned to a bin, averaged over all species. For MultiBin (red) the curves show average precision over 10 random starts of the clustering algorithm, and the error bars give the standard error of the mean. For AbundanceBin (blue) the curves show the average precision over the 5 samples in the dataset, and the dashed lines give the highest and lowest result of the 5. MultiBin achieves consistently better precision over both read lengths and over all sample complexities. AbundanceBin's performance exhibits high between-sample variability, and also deteriorate more rapidly as the number of species increase.</p

PLSA approximates mixture coefficient better than PCA.

<p>PCA and PLSA were performed on a simulated counts matrix with and different number of per-sample counts. The plot shows the average squared correlation coefficient between the true vectors and the three strongest principal components (in the case of PCA) or PLSA estimates . For each per-sample counts value 20 experiments were performed, and the plot gives the mean result and the standard error of the mean. The estimates obtained by PLSA show higher correlation with the true mixture proportions.</p

Significant correlations between components proportions and phenotypes.

<p>The predicted variables were regressed on the proportions of each component separately. The table gives the regression p-values, and in parentheses the empirical p-values obtained by permuting the components proportions times while keeping the phenotypes constant.</p

Examples for possible ancestry structures created for individuals and in order to test the relationship between them.

<p>The triangles under and represent their existing descendants, edges represent parent-offspring relationship.</p

Distribution of relationship scores under specific true relationships.

<p>Distribution of relationship scores under specific true relationships.</p

Souvenir Postcard Folder: Souvenir Folder of Beautiful Jacksonville, Florida

Souvenir Postcard Folder: Souvenir Folder of Beautiful Jacksonville, Florida; 1915 (134)https://digitalcommons.unf.edu/mette_postcardimages/1224/thumbnail.jp

Depicting cases where edge removal rules are required in polygamous pedigree reconstruction.

<p>Redundant graph edges are dashed red, correct edges in solid black.</p