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, please provide the environment information, such as sessionInfo()
    • incomplete: only R code scripts provided
  5. If it is about raw data processing, please 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
Error 'Processing Individual Data' for a meta-analysis
Raw Data Processing issue
Network analyst not working from past 3 days
Processing of my data is not working
The result might be misleading based on the normalized input
Cannot upload a Generic peak intensity table (no retention time)
How to input data into marker data profiling?
P-value changes in the same sample set under the same analysis parameters
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
Volcano-plot with vertical lines for FC at wrong place in downloaded image
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
Upset Diagram - Low quality sample detected
PCA plot bug
Bug in taxa abundance pdf export
Can MicrobiomeAnalyst work with non-bacteria dataset
Error in pathways and enrichment analyses
Exactly How is Mean Importance Measure Calculated for Multivariate Models?
QIIME2 tree taxonomy error
Error in uploading a file
Data upload error Microbiome Metabolomics
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?
Limited taxonomic levels
Raw data analysis
Permutation Test in PLSDA
Uploading error
MetaboAnalyst failed to create pdf report using online platform
About Microbiome Metabolomics function
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
Can not use QC_RLSC remove batch effect
Issue with Microbial Metabolomics
Error Differential Expression Analysis
Reads my paired-end library as single-read library! Why?
ANOVA2 Generation Issues Continued
Metadata upload problem in spectra processing
Wrong PCA Group labeling
Issues with DEG analysis
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