FAQ

Does the website save my expression data?

Absolutely not. Nor do we store your results. The only usage data we collect is through Google Analytics, which collects the time and duration of access, geolocation down to city level, and operation system information and so on. Google Analytics also seems to be trying to guess user demographics. We do not have access to user’s IP addresses.

“ID not recognized.”

iDEP website cannot recognize your gene IDs. Please try to use common gene IDs like Entrez gene ID, Ensembl gene ID, gene symbols, and so on. iDEP’s gene ID conversion is based on the information available at Ensembl. Alternatively, try to convert your data into such IDs.

My species is not covered in the list, can I still use the site?

Yes. You can still do exploratory data analysis and differential gene expression. To do enrichment analysis and pathway analysis, you can choose “NEW SPECIES” in the species drop down and then upload a gene set file in the GMT format. Note that gene IDs should match those used in the data file.

The website does not give me differentially expressed genes, and it said: “Failed to parse sample names to define groups.”

You either do not have replicates or the replicates are not clearly marked as “_Rep1”, “_Rep2” at the end of sample names. Please change column names of your data file.

I got an error message.

We would appreciate it if you could send us an email regarding that error with as much information as possible, include the first few lines of your data file. That will help us improve the software and serve our users better.

“No significant pathway found.”

Using the current choices of options, iDEP does not find significant pathways. You can try to lower the FDR cutoff or change the gene set database.

My results stay the same when I switch databases while using ReactomePA.

When you choose ReactomePA, the Bioconductor package uses its own gene set database based on Reactome.