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Sequencing coverage depth was compared between sample types using two-tailed t-tests assuming unequal variance.
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The extents of methylation of LINE1 and ALU-Yb8 were compared between donors and recipients, stratified by sample type, using the nonparametric Mann–Whitney U test in order to limit the influence of outlier points.
ANOVA analysis was used to identify microRNAs differentially expressed between sample types and P values were adjusted using the Benjamini-Hogberg correction method.
In total "change" proteins were identified at FDR of 1% and normalized for quantitative analysis using the Scaffold4 software package using log2 values to compare between sample types.
The χ test was used for differences in rates of detection of FC and Bacteroidales markers between sample types representing different exposure pathways.
The use of TMT-sixplex isobaric tags allowed for direct, quantitative comparison between sample types.
We found no difference between sample types.
We discuss two such approaches: 1) the splicing index, which compares probeset inclusion across samples after normalizing by gene expression levels, and 2) two-way ANOVA, where the interaction term between sample type and probeset can be used to indicate differential inclusion of probesets within transcripts.
Fisher's exact test was used to analyse association between sample type and LRP1 expression level.
I tested for differences in overall shape variation (i.e., convex hull volumes) between the two habitat types using independent samples t-test assuming unequal variances.
However, no modulation was observed between samples types.
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