MetImp 1.2

News & Updates

Added set seed options at June/27/2018;

Elaborated the required data format at June/18/2018;

Added a new module for MNAR imputation (GSimp) at May/21/2018;

MetImp was started on March 2017!


Contact

runmin@hawaii.edu

jingyew@hawaii.edu


Citations

Please cite us :

10.1038/s41598-017-19120-0 10.1371/journal.pcbi.1005973

Introduction

MetImp is a web tool for -omics missing data imputation, especially for mass spectrometry-based metabolomics data from metabolic profiling and targeted analysis.

There are three types of missing values in Metabolomics: missing completely at random (MCAR), missing at random (MAR), and missing not at random (MNAR). We recommend a comprehensive approach for handling missing values:

(1) Analyze the possible reasons of missing values: whether they are MNAR/MAR, or MNAR;

(2) If necessary, check raw data and/or adjust parameter settings of data preprocessing in order to fill back certain missing values in an accurate way;

(3) Apply missing filtering to remove those unreliable variables with unacceptable number of missing values;

(4) If missing value imputation is needed for your data, choose an appropriate method;

(5) MetImp provides:

A. Group-wise missing filtering: 0%~100% adjustable, 80% is the default proportion ;

B. For MCAR/MAR: we provide RF, SVD, kNN, Mean, Median imputation, and RF is default;

C. For MNAR: we provide GSimp, QRILC, HM, Zero, Binary imputation, and GSimp is default.

For the imputation evaluation pipeline, please visit: https://github.com/WandeRum/MVI-evaluation

Upload your data


Or download our example data
Raw data overview:
Uploading...

MCAR imputation

If checked, variables with non-missing proportion less than the threshold will be removed in the output.
Imputed data overview:
MCAR imputing...

MNAR imputation

If checked, variables with non-missing proportion less than the threshold will be removed in the output.
Please note that GSimp is a Markov Chain Monte Carlo (MCMC) based algorithm, which is time-consuming especially for large datasets.
Imputed data overview:
MNAR imputing...

News & Updates

Added set seed options at June/27/2018;

Elaborated the required data format at June/18/2018;

Added a new module for MNAR imputation (GSimp) at May/21/2018;

MetImp was started on March 2017!


Contact

runmin@hawaii.edu

jingyew@hawaii.edu


Citations

Please cite us :

10.1038/s41598-017-19120-0 10.1371/journal.pcbi.1005973

App Info

Version 1.2

Built using Shiny by R and RStudio

License

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License

Support

For sending comments, suggestions, bug reports of MetImp, please email to Runmin Wei (runmin@hawaii.edu)

References

Stekhoven, Daniel J., and Peter Bühlmann. "MissForest—non-parametric missing value imputation for mixed-type data." Bioinformatics 28.1 (2011): 112-118.

Hastie, Trevor, et al. "Imputing missing data for gene expression arrays." (1999): 1-7.

Troyanskaya, Olga, et al. "Missing value estimation methods for DNA microarrays." Bioinformatics 17.6 (2001): 520-525.

Lazar, Cosmin. "imputeLCMD: a collection of methods for left-censored missing data imputation." R package, version 2 (2015).