Please be patient when opening the files. It may take a while before all embedded tables and plots are uploaded if the file size is large.

1 Introduction

This report consists of five parts in separate html-documents created in R Markdown that contains embedded files with raw data and quality control parameters from the lab of BEVITAL AS.
The report allows the generation of Excel files covering the whole data set, and also creates summery statistics and graphics, as well as details about assay performance and reasons behind missing data points, if any.

Content

Part 1
Section 2 describes key parameters of the metabolites that are routinely analyzed at BEVITAL and reported here.
Section 3 contains the metabolomics data from our analyses of your samples. Here, you can download result files in several formats.
Section 4 provides descriptive statistics for raw (non-imputed) data.

Part 2
Section 1 contains data sets generated using different imputation methods for left-censored missing values (missing not at random), if any.
Section 2 provides descriptive statistics for imputed data.
This part is not included in the report if there are no missing values or the conditions for left-censored missing value imputation are not met.

Part 3
This part contains tables and plots showing missing data points, if any, and reasons for missingness.
This part is not included in the report if there are no missing values.

Part 4
This part reports quality control parameters from the lab, such as coefficients of variation.

Part 5
This part presents the data in descriptive raincloud, correlation, and network plots that can be downloaded.
This part may not be included in the report if only a few metabolites have been measured.

Tables
All tables are downloadable in different formats and assigned unique file names.
Remember to scroll sideways to see all the columns in the tables.
How tables are displayed varies with the browser used (Internet Explorer / Edge / Chrome / Firefox / Safari).
In some browsers, the column widths and table headers may not adjust properly before clicking the “Next” button or change the number of entries.

Figures
How figures are displayed and can be downloaded also varies with the browser used.
When using Safari on Mac, hover on the lower part of the windows containing figures to show the download buttons.
If you do not see one or more plots, try another browser.
We recommend using Firefox (first choice) or Chrome. These browsers provide the same functionality on PC and Mac.
We emphasize that the plots in this report are for descriptive purposes only and that different subgroups in the samples have not been taken into account.
If the number of data points is large, then some of the plots may be excluded from the report to reduce the file size.

Missing data
Missing data are common in many studies and are often not handled properly. This may result in reduced statistical power or biased results. This report helps you to handle missing data points, if any. First, the reasons for missingness are coded in the coded data set (part 1, section 3.2) and further specified in part 3. Secondly, the frequency and proportion of missing values for each variable are summarized in part 3. Third, we have generated data sets (part 2, section 1) where left-censored missing data (missing not at random) are imputed by different methods. Notably, missing values should be imputed separately for each subgroup, if any. This is done in the lab data report only when we have information about group allocation specified in a separate column in the Excel file following the samples.

Reference
Please refer to BEVITAL AS and our website in the method section when publishing data measured at our lab.

2 Metabolites

2.1 Description

2.1.1 All

All platforms that include measured metabolites

Reported values for serum/plasma.
Reported values are not strictly normal reference range, which depends on the population, and several factors, including age, gender, ethnicity and procedures for sample handling and analytical technology. Reported values are informed by concentrations that we and others have observed or reported in various cohorts of healthy subjects.
See all the performance data on our website.
KTR (platform B or D): see description on our website.
PAr (platform D): see description on our website.
HKr (platform D): see description on our website.

Abbreviations:

  • LOD: limit of detection (method validation performance data)
  • wdCV: within-day CV (method validation performance data)
  • bdCV: between-day CV (method validation performance data)
  • ICC: intraclass correlation coefficient

2.1.2 A

Platform A
TCA metabolites and intermediates | Short-chain fatty acids (SCFAs)

2.1.3 B

Platform B
Amino and carboxylic acids

2.1.4 C

Platform C
Choline derivatives | Charged, methylated or sulfur amino acids | Short- and medium-chain acylcarnitines

2.1.5 D

Platform D
Kynurenine pathway | B-vitamins (B1, B2, B3, B6)

2.1.6 E

Platform E
Folate species and catabolites

2.1.7 F

Platform F
Folate (vitamin B9) and cobalamin (vitamin B12)

2.1.8 G

Platform G
Protein biomarkers and variants

2.1.9 H

Platform H
Lipid-soluble vitamins | Long-chain acylcarnitines

2.1.10 Derived ratios/indexes

Derived ratios/indexes
This table contains ratios/indexes calculated from the measured metabolites.

If a calculated ratio/index is derived from more than one platform, only one of them is included in the result files.

2.2 Zero values

For metabolites with biological meaningful zero values, such as pyridoxine (PN), nicotinic acid (NA), cotinine (Cot), and trans-3-hydroxycotinine (OHCot) in platform D, folic acid (FA) in platform E, and vitamin D2 (vitD2) in platform H, LODs (limits of detection; coded with -3 in section 3.2) are not treated as missing values, but given as zeros (0).

3 Data

Data are downloaded by clicking the table button(s) for your preferred file format(s).

3.1 Data set excluding codes for missing values


Here, the table cells are empty if data points are missing. Reasons for missingness are specified in part 3.
Platforms are designated by the uppercase letters after the two punctations in column headings.
SampleID may be a combination of: 1) the lab’s ‘SampleID’ (before the punctations) and the project’s ‘SubjectID’ (after the punctations) or 2) the lab’s ‘SampleID’ (before the underscore) and the lab’s ‘SeriesNo’ (after the underscore).
As most circulating metabolites fit a log-normal (multiplicative) distribution equally well or better than a normal (additive) distribution, we strongly recommend to log-transform the positive valued continuous outcome data, which are often positively skewed, before the data exploration and statistical analyses.

3.2 Data set including codes for missing values


Here, there are no empty table cells. Missing data points are indicated by negative numeric codes for reasons of missingness. These codes are explained in part 3.
Platforms are designated by the uppercase letters after the two punctations in column headings.
SampleID may be a combination of: 1) the lab’s ‘SampleID’ (before the punctations) and the project’s ‘SubjectID’ (after the punctations) or 2) the lab’s ‘SampleID’ (before the underscore) and the lab’s ‘SeriesNo’ (after the underscore).
As most circulating metabolites fit a log-normal (multiplicative) distribution equally well or better than a normal (additive) distribution, we strongly recommend to log-transform the positive valued continuous outcome data, which are often positively skewed, before the data exploration and statistical analyses.

4 Descriptive statistics

4.1 Pooled data


Be aware of metabolites with biological meaningful zero values. Here, gMean is usually equal to zero, and it will not be possible to calculate gSD.

Abbreviations:

  • n: numbers of samples successfully measured and quantified (i.e., not including missing data points)
  • IQR: interquartile range; measures the spread of the middle half of the data when values are ordered from lowest to highest
  • gMean: geometric mean
  • gSD: geometric SD
  • gSDrange: geometric SD range (1 SD range); calculated by dividing and multiplying the geometric mean (gMean) with the geometric SD factor (gSD) to obtain the lower (gSDlower) and upper (gSDupper) limits, respectively

4.2 Grouped data


This table is empty if we have no data on group allocation.
Be aware of metabolites with biological meaningful zero values. Here, gMean is usually equal to zero, and it will not be possible to calculate gSD.

Abbreviations:

  • n: numbers of samples successfully measured and quantified (i.e., not including missing data points)
  • IQR: interquartile range; measures the spread of the middle half of the data when values are ordered from lowest to highest
  • gMean: geometric mean
  • gSD: geometric SD
  • gSDrange: geometric SD range (1 SD range); calculated by dividing and multiplying the geometric mean (gMean) with the geometric SD factor (gSD) to obtain the lower (gSDlower) and upper (gSDupper) limits, respectively