Requirements for Troubleshooting

** Help Us Help You: Detailed Reports Solve Issues Faster**

Just like a doctor cannot provide a diagnosis without an examination, our team cannot fix a problem we cannot see. To troubleshoot effectively, we need to reproduce the issue. Since most errors are specific to your unique data or steps, please provide a step-by-step description of your actions so we can find a solution quickly.

Make sure all the information below are provided in your post:

  1. Which tool and which module
    • incomplete: only tool name provided
  2. Provide a copy of your data (the actual data file, not a screenshot image of the data), or indicate which example data you used
    • For large data, please provide a link to Dropbox, Google Drive, etc
  3. Document all steps leading to the issue. Sometimes screenshots may be necessary
    • incomplete: only vague description provided
    • incomplete: did not give method & parameter selections on each page prior to the issue
  4. If it is about using R packages, you also need to provide the environment information, such as sessionInfo()
    • incomplete: only R code scripts provided
    • unsupported: R package in Windows OS. Our development enviroment is Linux and some OS-specific low level issues are hard to debug. In general, we recommend Linux OS or using our web platform.
  5. If it is about raw data processing, please also describe how the data were collected (instrumentation, etc).
    • incomplete: only Job ID or screenshot is provided

If your questions are not answered, it is probably because we don’t know how to reproduce the issue, or we don’t have time to guess all possible scenarios.

Heading

Problem with raw data (fastq) processing
Processing of my data is not working
Raw Data Processing issue
Network analyst not working from past 3 days
Error 'Processing Individual Data' for a meta-analysis
Error in Metadata upload
Error in uploading a file
Generate report
Uploading error
Error Failed to parse your taxonomy file. Please check the file format!
Data upload error Microbiome Metabolomics
Read.TextData : object 'anal.type' not found
PCA plot bug
MetaboAnalyst failed to create pdf report using online platform
MetaboAnalyst 6.0 Volcano plot error in downloading
Raw data analysis
Issue with Microbial Metabolomics
Inconsistency between selected files and metadata provided
About Microbiome Metabolomics function
Troubleshooting in functional analysis
Exactly How is Mean Importance Measure Calculated for Multivariate Models?
Error in Downloading Analysis Report in Pathway Analysis
Can not use QC_RLSC remove batch effect
3D PCA drag function not working
Can't upload data
QIIME2 tree taxonomy error
Metabolite ID Conversion NOT working now?
Identification of significant features from individual omics
MetaboAnalyst report
Could not proceed beyond the Analysis Overview step in NetworkAnalyst
Give us details!
Metadata upload problem in spectra processing
Cannot upload a Generic peak intensity table (no retention time)
Error uploading data to the MetaboAnalysis Network
Plots not loading for [one factor] statistical analysis
Why I am getting the message: "The result might be misleading based on the normalized input"
OPLS-DA down
Error in Uploading to MicrobiomeAnalyst for 16s rRNA analysis
The t-test cannot be used
/Problems with loading numerical/continuous metadata in MicrobiomeAnalyst
Permutation test in Biomarker Analysis
PICRUSt Greengenes reference OTUs files
Error in Normalisation
Very long analysis
Upload error in Multiple expression tables: #CLASS unrecognition
Metaboanalyst Heatmap error - use only group average
Volcano-plot with vertical lines for FC at wrong place in downloaded image
Previously working data set error
Job seems to be stuck
Marker data profiling error when uploading Mothur files
Upload biom file
PCA 2D scores plot bug?
OPLSDA not working in Metaboanalyst
Limited taxonomic levels
Error in pathways and enrichment analyses
A total of 1295 significant features were found
PerformBatchCorrection error
Error in Marker Data Profiling
Microbial metabolomics not working
Can MicrobiomeAnalyst work with non-bacteria dataset
Error downloading raw data results
P-value changes in the same sample set under the same analysis parameters
Unknown error in two-way ANOVA normalisation
Difficulty loading data into Omics
Can't finish data loading for Functional Analysis
Error in editing groups
Prolems with metadata covariates
Error in sequencing data filtering and trimming
Issue using association analysis and Diversity overview
An error in multiple expression tables
[HELP] Why I'm not seeing compounds ID when analyze data in metaboanalyst?
Beta diversity inconsistent results between 2D and 3D plot
Getting error message in R
Error uploading transcriptomics in OmicsAnalyst
Paired analysis of differential relative abundance
Functional Meta analysis
Error appeared when trying to do the Multiple Linear Regression with Covariate Adjustment
Error in Read16SAbundDataMeta()
Metanalysis-linear regression with covriate adjustment
Error in Metadata upload
Error in data upload in statistical meta-analyses!
Issue while performing single gene expression table in express analyst
UpSet Plot not plotting all datasets
Argument 'length.out' must be of length 1
When I do the statistical analysis, this page indicates an unknown error that is unique to your data and parameters
Functional analysis - filtering broken?
PCA with gene expression data
Metabolon data sheet upload
Sparcc
HMDB names not valid
The database you have selected is not matched/found!
Meta data/time series analysis not working
Tax4Fun
how does auto-optimized parameters works
The alpha diversity Chao1 values differ from the values calculate by R
MEBA analysis
MetaboAnalyst 6.0 is unable to perform T-tests and other functions related to T-tests correctly!
Error in batch effect correction tool
Can not perfomr t.test in MetaboAnalyst
Statistical Analysis [metadata table] 500-Internal Server Error
Issue with Single Gene Expression Table Data Processing
Error when doing comparative analysis
Feature Box Plot uses only raw reads, not rarefied (FDR) ones
An error was presented when I tried to uploaded my files for meta-analysis
Ridgeline Chart not working
Issue uploading a phylogenetic tree
Pathway Analysis - MetaboAnalyst 6.0
Enrichment analysis
Error of duplicates when uploading files for Tax4Fun2 analysis
Microbiome metabolite analysis - not proceeding after data upload
I cannot save the high reso png result in Multivariate ROC curve based exploratory analysis
MetaboAnalyst 6.0 Pathway analysis
Any Changes for Cluster Methods of MetaboAnalyst 6.0 A-single factor analysis? (compare to 5.0)
MetaboAnalyst Pathway analyses issue
Different p-values in wilcox rank sum test and enrichment analysis
Error in Linear models with covariate adjustments
Error in Linear models with continuous data
Metabonalyst - data size
Use the metaboanalyst 5 instead of metaboanalyst 6
Functional Analysis [LC-MS] .txt File Formatting Issue
Functional Analysis [LC-MS] error
MEBA not working - data unbalanced
Error in creating reference metabolome
Enrichment Analysis and Pathway Impact
Network view doesn't work
About HEATMAP error - use only group average
6.0 - batch-effect - broken website?
Volcano plot on bulk seq data
Interpretation of NES Values
Problem with MS1 + DDA spectra processing
Impossible to downloas image of vulcano plot
Data upload unknown error
Query mass in mummichog outputs not matching m.z inputs
MIcrobiomeAnalyst error in parsing data as numerical- possible reason: comma as decimal separator
Dimension reduction failed
Error when uploading reference library during enrichment analysis
Data upload issue
Time-series analysis: data not recognized as paired
Microbiome and metabolome integration - file upload
Unknown error that is unique to your data and parameters but table and metadata seems correct
Problem with understanding results from Multi-Factor Analysis
Error during alpha diversity analysis
Error transferring data, how can I solve it?
Unknown error occurred
Pairwise comparison table error in alpha and beta diversity
I could not perform the heatmap correlation since yesterday. Please let me know what will be the problem? Thank you
Fetal error: Using OrthoPLS-DA analysis
Issue with Data Processing in MetaboAnalyst 6.0 – Seeking Guidance
Disease pathways enrichment analysis
Out of memory error
Raw data processing - paired end
Normalization issue (rarefaction)
Data Filtering & Normalization Error messege
Error with paired-end data in raw data processing
Issues for Raw Sequencing Data Upload
Error:One sample name was not included in the OTU/ASV abundance table
Error uploading proteomics, metabolomics, lipidomics data
Why won't it let me colour by 'experimental factor'?
Raw reads processing
Heatmap question
Interactive Pie Chart Exploration only shows sex differences but not age and organ-related differences.
Wrong taxa labels
Heat tree not labelled
Confusion Regarding Metabolite "Expression" in OmicsNet.ca
Fastq.gz files will not upload
Volcano plot: missing data in the linked detailed data table
Volcano plot: impossible to download the image
Error in metadata file
Data upload problem
Compound IDs not matching with the MetaboAnalyst database
LC-MS database selection not working. It says peak construction failed at network construction step
Error: please upload your data first, but I've already uploaded the data
Reference Metabolome in pathway analysis
Help Needed with Functional Meta-Analysis Data Upload Issue
Spectra processing error
Whole matrix - format for GSEA
Required data format
One factor PCA 2D Scores Plot does not work
Unable to perform permutation for PLS-DA analysis
Error reading meta data when uploading file
Inability to perform metabolic pathway analysis on PLS data
Pval Issues and Obtaining more detailed enrichment analysis results
2 treatment, 5 point timecourse, heatmap from csv
Joint pathway analysis for Candida albicans data
Error: Differential analysis failed for metabolomics data using current parameters!
Error of OPLS-DA
Error Message in Data Upload on Microbiome Analyst
Issue processing QTOF data with asari
Joint pathway analysis-no gene list
Heatmap does not complete
Network analysis
One-way ANOVA Test not working
Installation issue with MetaboanalystR 4.0 in R v. 4.5.0
Unknown Upload Error using Test Data
oPLSDA and sPLSDA do not work
Exporting normalized data
Assistance Required - Gene List Not Recognized in Joint Pathway Analysis for Arabidopsis thaliana
Volcano plot: impossible to download the image
"Calculate.ANOVA.posthoc" not ound error
Multivariate Empirical Bayes Analysis of Variance (MEBA) for Time Series -- unable to load
Enrichment analysis fails when using SMPDB database
Pathway analysis - error with uploading metabolite list
The symptoms of oPLSDA and sPLSDA not working
Data formatting error, generic error, but my data seems to be formatted correcly
"Unknown error happened during data normalization process!"
Normalization related issue
Imputation result is not displayed in OPLSDA
Failed to download volcano image
The PCA function doesn't work
The 3D plots for PCA and OPLS-DA could not be generated, and the volcano plot could not be downloaded. Please assist with resolving this issue
ISSUE with PCA in web server
Issue to log-transforming data on pathway analysis
The statistics tools don't take the output from the initial data QC steps
ROC curve shows AUC = 1 for nearly all features despite variability in univariate results
Using dose/response modeling with pre-normalized data
ANOVA2 and MEBA doesn't work
Missing value processing
Metaboanalyst volcano plot
Issues Installing MetaboAnalystR Package
Statistical analysis one factoring data upload
Pathway analysis is not working, Data normalization image is not showing and processing error occupied
Statistical analysis (one factor) totally broken
Pathway analysis is not working, Data normalization image is not showing and processing error occupied
ExpressAnalyst is not loading past the normalization page
P values the same in multiple comparisons?
Metabolomics data in Omicsnet are unavailable
Out of memory error when processing small MS1 dataset
Data upload for Tax4FUN
Taxonomy data in .biom file not available
Normalization Bug
Differences in the results between the newest version and the previous one
Excluded Samples Still Appear in PCA
Data editor for excluding/including samples is not working properly since two weeks
ANOVA analysis is misassigning groups if the uploaded data is not sorted by group in the one factor statistical module
Is PCA down?
Web MetaboAnalyst PCA crashes
"Unknown Error Occurred" uploading .csv files, or using examples
Problems with performing lineal models in the Time-series + one factor Time-series + one factor design
Missing value filling failed
Facing Issue in getting plots?
How are raw p-values calculated in MetaboAnalyst and why are they different to Excel?
MicrobiomeAnalyst Model loading
Error failed to perform data filtering
Enrichment analysis not working recently
Microbiome Analyst own examples not working
Alpha/Beta diversity modules failing on MicrobiomeAnalyst (Marker Data Profiling)
SNP Filtering & Harmonization failed to process
Platform instability: data analysis is offline and groups filtering broken, is there a status update/ETA for fix?
Problem in Pathway analysis (with Concentration Table)
Visualisation problems after data file uploaded successfully
2- and 3- phosphoglyceric acid are not taking into account into the pathway analysis
Wrong PCA Group labeling
Discrepancy in Joint Pathway Analysis Results - Enrichment vs. Over-representation
Bug in Abundance Profiling Visualization by Multiple Factors
Installing MetaboAnalystR in Linux
Pathway Analysis "Unknown Error"
Error in data upload in statistical meta-analyses!
Result about Lefse show unknown genus(?)
Data upload error using "marker data profiling"
Miscolored PCA and PLS-DA Plots
Upload a gene expression table - Error
How to input data into marker data profiling?
Error in the color use of the Integrated Pathway Activity Profile plot
Heat tree colour scheme
Bug in taxa abundance pdf export
Error in Marker Data Profiling
SparCC error
An error when I tried to uploaded my files for meta-analysis
Heattree image shows less number of features than the result table
Group adjustment pop-up is blank, cannot be modified
ErrorProcessing Faild, unable to finish the job!
TAX4Fun2
After normalization, the document shows that the variety of compounds decreases
Networkanalyst data input
Error uploading the file in expressanalyst, while using my ngs file
Invalid phylogenetic tree file when running beta diversity test with UniFrac distance
Multiple samples - Proteomic data
Upset Diagram - Low quality sample detected
Bug in taxa abundance pdf export
Upload error in Multiple expression tables: #CLASS unrecognition
Single-ended
Unknown error in the pathway enrichment analysis
Enriched pathway with metabolites connection Figure export
Failed to perform normalisation
How to validate kallisto reference genome in database folder?
Permutation Test in PLSDA
Error uploading FASTQ onto microbiome analyst
Tax4fun2 analysis in MicrobiomeAnalyst yields no results.
Significant gene list download
Troubleshooting This page indicates an unknown error that is unique to your data and parameters
Problems with tax4fun
Malfunction
General Error Landing
General Error Landing
Sparse PLS-DA not working
Miscolored PCA and PLS-DA Plots
Data negative
"Sample names match (metadata vs. OTU table): No" issue
One Factor Statistical Analysis PLS-DA Permutation Test Do Not Display Or Download
Functional Prediction - PICRUSt (Greengenes) - Tax4Fun (SILVA) using the QIIME outputs
Functional Prediction - PICRUSt (Greengenes) - Tax4Fun (SILVA) using the QIIME outputs
As a result of correlation analysis, arrangement and picture download are not available
Data upload failed
What does this"Possible causes of error (last one being the most relevant):"mean?
Batch effect correction
How I can see the boxplots of significant features in the t-test?
Errors with replicates and groups in "one factor statistical analysis"
Why can I not see genera in my stacked bar drop down list
Why can I not see genera in my stacked bar drop down list
Editing adducts in functional analysis creates unknown error
Heatmap does not show a chromatic scale correspondent to data
Error Differential Expression Analysis
Reads my paired-end library as single-read library! Why?
ANOVA2 Generation Issues Continued
Issues with DEG analysis
Why MetaboAnalyst 5.0 can not be used ?