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Fig. 4 | Microbiome

Fig. 4

From: Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

Fig. 4

Comparison of SCML and normalization by qRT-PCR-derived total number of 16S rDNA copies to all background OTUs. Observed log2 ratio versus expected log2 ratio of all background bacteria OTUs for all pairwise sample comparisons after (a) SCML by S. ruber and (b) normalization by qRT-PCR derived total 16S rDNA copy number. The data is binned to hexagons because of the high number of data points. The colour of each hexagon represents the percentage of all counts at the corresponding level of expected log2 ratios contained in each bin. Bins that contributed to less than 0.05 percent for each level of expected log2 ratio are omitted. The purple diagonal represents the identity, which represents the expected log2 ratios by design. The box-plots in (c) summarize the error between the expected and observed log2 ratios for the four different approaches. The smaller this error, the better calibrated the ratios are. Variances of the log2 differences are 3.65, 2.01, 1.28 and 1.18 as derived from relative abundances, counts calibrated for differences in total number of 16S rRNA gene copies, SCML (by S. ruber) and combined SCML (by S. ruber, A. acidiphilus and R. radiobacter), respectively

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