(a) Inputs are two LC-MS datasets of unlabeled metabolic features (rows) identified by their , RT, and feature intensities across biospecimen samples. Both studies can have differing numbers of …
(a) Initial LC-MS dataset taken from the EXPOsOMICS project with , RT, and feature intensities of metabolites identified in cord blood across newborns. (b) Newborns (rows) are split into two …
(a) Ground-truth matchings, and matchings inferred by metabCombiner, M2S, GM, and GMT. Pairs of datasets are generated for three levels of overlap (low, medium and high), with a medium noise level …
The noise level corresponds to different values of and . High, medium, and low noise level correspond to and (1, 1) respectively. We run 20 simulations for each setting.
The feature intensities of both datasets are centered and scaled to have means of 0 and standard deviations of 1. The average precision and recall of the three methods are computed on 20 randomly …
(a) Dimensions of the three EPIC studies used. For each ionization mode, the cross-sectional (CS) study is aligned successively with the hepatocellular carcinoma (HCC) study and the pancreatic …
Each scatter plot represents the mean feature intensities of manually matched features from the validation subset. Each dot represents a pair of manually matched features. The axis represent the …
Venn diagrams are not up to scale.
Each dot correspond to a candidate matched pair after the first step of GM ( constrained GW matching), before the RT drift estimation and RT-based filtering.
(a) Loftfield study implemented a discovery step, examining the relationship between alcohol intake and metabolic features in the CS study. The significant features in CS were manually matched to …
The first setting, labelled ‘Scores’ correspond to the design of our main analysis, where 100 randomly selected true pairs are supplied to metabCombiner to set the scoring weights automatically, but …
Features from the CS study (163 features in positive mode, 42 features in negative mode) were manually investigated for matches in the HCC and PC studies.
Study | Manual matches found in positive mode | Manual matches found in negative mode |
---|---|---|
Hepatocellular carcinoma (HCC) | 90 | 19 |
Pancreatic cancer (PC) | 66 | 28 |
95% confidence intervals were computed using modified Wilson score intervals (Brown et al., 2001; Agresti and Coull, 1998).
Method | Precision | Recall | Precision | Recall |
GromovMatcher | 0.989 (0.939, 0.999) | 0.978 (0.923, 0.996) | 0.903 (0.813, 0.952) | 0.985 (0.919, 0.999) |
M2S | 0.967 (0.908, 0.991) | 0.978 (0.923, 0.996) | 0.855 (0.759, 0.917) | 0.985 (0.919, 0.999) |
metabCombiner | 0.961 (0.868, 0.993) | 0.544 (0.442, 0.643) | 0.967 (0.833, 0.998) | 0.439 (0.326, 0.559) |
95% confidence intervals were computed using modified Wilson score intervals (Brown et al., 2001; Agresti and Coull, 1998).
Method | Precision | Recall | Precision | Recall |
GromovMatcher | 0.950 (0.764, 0.997) | 1.000 (0.832, 1.000) | 0.929 (0.774, 0.987) | 0.929 (0.774, 0.987) |
M2S | 1.000 (0.824, 1.000) | 0.947 (0.754, 0.997) | 0.931 (0.780, 0.988) | 0.964 (0.823, 0.998) |
metabCombiner | 0.875 (0.529, 0.993) | 0.368 (0.191, 0.590) | 1.000 (0.845, 1.000) | 0.750 (0.566, 0.873) |
Metric | Low overlap | Medium overlap | High overlap |
---|---|---|---|
Precision | 0.831 | 0.917 | 0.947 |
Recall | 0.934 | 0.933 | 0.939 |
95% confidence intervals were computed using modified Wilson score intervals Brown et al., 2001; Agresti and Coull, 1998.
Method | Precision | Recall | Precision | Recall |
GromovMatcher | 0.988 (0.937, 0.999) | 0.944 (0.876, 0.997) | 0.873 (0.776, 0.932) | 0.939 (0.854, 0.976) |
M2S | 0.967 (0.908, 0.991) | 0.978 (0.923, 0.996) | 0.855 (0.759, 0.917) | 0.985 (0.919, 0.999) |
metabCombiner | 0.979 (0.889, 0.999) | 0.511 (0.410, 0.612) | 0.926 (0.766, 0.987) | 0.379 (0.271, 0.499) |
(a) Positive mode | ||||
Method | Precision | Recall | Precision | Recall |
GromovMatcher | 0.950 (0.764, 0.997) | 1.000 (0.832, 1.000) | 0.964 (0.823, 0.998) | 0.964 (0.823, 0.998) |
M2S | 1.000 (0.824, 1.000) | 0.947 (0.754, 0.997) | 0.931 (0.780, 0.988) | 0.964 (0.823, 0.998) |
metabCombiner | 1.000 (0.566, 1.000) | 0.263 (0.118, 0.488) | 1.000 (0.785, 1.000) | 0.500 (0.326, 0.674) |
(b) Negative mode |