Requirements for Troubleshooting

For troubleshooting, we need to reproduce the issue. It is very hard to perform “remote diagnosis” with limited information, as many errors are specific to your data and your operations. Also keep in mind that the forum is maintained based on our spare time .

Please 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 (actual data that leads to the error, 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
  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 different scenarios).

Problem with raw data (fastq) processing
Processing of my data is not working
Raw Data Processing issue
Error 'Processing Individual Data' for a meta-analysis
Network analyst not working from past 3 days
Generate report
Cannot upload a Generic peak intensity table (no retention time)
Metadata upload problem in spectra processing
Data upload error Microbiome Metabolomics
Limited taxonomic levels
Raw data analysis
About Microbiome Metabolomics function
The result might be misleading based on the normalized input
P-value changes in the same sample set under the same analysis parameters
Can not use QC_RLSC remove batch effect
Issue with Microbial Metabolomics
MetaboAnalyst failed to create pdf report using online platform
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
PCA plot bug
Upload error in Multiple expression tables: #CLASS unrecognition
Bug in taxa abundance pdf export
Can MicrobiomeAnalyst work with non-bacteria dataset
Error in pathways and enrichment analyses
Upload error in Multiple expression tables: #CLASS unrecognition
Exactly How is Mean Importance Measure Calculated for Multivariate Models?
QIIME2 tree taxonomy error
Error in uploading a file
Give us details!
Unknown error in the pathway enrichment analysis
Failed to perform normalisation
Error Failed to parse your taxonomy file. Please check the file format!
How to validate kallisto reference genome in database folder?
Permutation Test in PLSDA
Uploading error
OPLSDA not working in Metaboanalyst
Error uploading FASTQ onto microbiome analyst
Tax4fun2 analysis in MicrobiomeAnalyst yields no results.
PICRUSt Greengenes reference OTUs files
Significant gene list download
Troubleshooting This page indicates an unknown error that is unique to your data and parameters
PerformBatchCorrection error
Problems with tax4fun
Error in Downloading Analysis Report in Pathway Analysis
Marker data profiling error when uploading Mothur files
Upload biom file
Error in Uploading to MicrobiomeAnalyst for 16s rRNA analysis
General Error Landing
General Error Landing
Sparse PLS-DA not working
Troubleshooting in functional analysis
Miscolored PCA and PLS-DA Plots
3D PCA drag function not working
Data negative
"Sample names match (metadata vs. OTU table): No" issue
Can't upload data
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"
Error in Marker Data Profiling
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
Job seems to be stuck
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
Error downloading raw data results
Issues with DEG analysis
Could not proceed beyond the Analysis Overview step in NetworkAnalyst
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
Very long analysis
An error in multiple expression tables
Read.TextData : object 'anal.type' not found
[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
Microbial metabolomics not working
Inconsistency between selected files and metadata provided
Paired analysis of differential relative abundance
Metabolite ID Conversion NOT working now?
Functional Meta analysis
Difficulty loading data into Omics
Wrong PCA Group labeling
/Problems with loading numerical/continuous metadata in MicrobiomeAnalyst
Unknown error in two-way ANOVA normalisation
Bug in Abundance Profiling Visualization by Multiple Factors
Installing MetaboAnalystR in Linux
Result about Lefse show unknown genus(?)
Miscolored PCA and PLS-DA Plots
Upload a gene expression table - Error
How to input data into marker data profiling?
Bug in taxa abundance pdf export
Error in Marker Data Profiling
SparCC error
Heattree image shows less number of features than the result table
Group adjustment pop-up is blank, cannot be modified
Error uploading data to the MetaboAnalysis Network
ErrorProcessing Faild, unable to finish the job!
Volcano-plot with vertical lines for FC at wrong place in downloaded image