Sentence examples for between the sample types from inspiring English sources
Next, we calculated the absolute difference and the percent difference between the sample types to estimate systematic bias.
Table 3 lists the statistics applied to evaluate the agreement between the sample types.
Each comparison was filtered to find spots having > 1.45-fold change in average normalized volume expression between the sample types.
In comparison, culture concordance between the sample types was seen in only 19 cases (12%), driven largely by no detection reported in the BSI culture results.
However, even when using the full set of unfiltered TCGA samples, no modulation of 5p-to-3p expression ratios or isomiR distribution was found between the sample types.
In order to visualize the relationships between the sample types, we performed unsupervised Principal Component Analysis using the 782 significant genes.
This algorithm superimposes gene-expression values with corresponding network proteins, begins from every protein (seed) in the PPI network, and greedily appends interactions to identify the subnetwork starting from each seed whose mean expression for each sample best discriminates between the two sample types (In our case, the sample types are T-ALL and nonleukemia/healthy conditions).
For the DDTs and PBDEs, the proportion of samples with concentrations above LOD varied between 3.7 and 45.5% depending on the sample type.
RNA degradation plots seemed to reflect to some extent the bimodality between samples types although individual variability was clearly larger than the variations caused by the sample type (see Figure 2).
Similarly, no statistically significant differences were found in the central tendencies of any of the REE between the two sample types (Wilcoxon rank-sum test for location shift; (P approx 1) for all elements, corrected for multiple comparisons).
For an overview comparison between the different sample types, we merged the results found in the different faecal communities and displayed the overlapping genera within stress and normal groups in the Venn diagram as shown in Fig. 4.
