Frequently Asked Questions (FAQ)

Why un-normalized counts?

DESeq2 requires count data from RNA-Seq (or another high-throughput sequencing experiment) as a matrix of raw values. Non-integer values are converted to integers so DESeq2 can run. The values must be un-normalized, since the DESeq2 model corrects for library size internally — do not use counts scaled by library size. For already-normalized counts, use edgeR or limma instead.

Why am I getting an error while uploading files?

  • DEBrowser supports tab-, comma-, or semicolon-separated files. Spaces or non-numeric characters inside numeric columns cause upload errors — remove them first.

  • Using the same gene name more than once also fails. This often happens after opening a file in Excel, which auto-converts some gene names to dates (e.g. SEP9 → SEP.09.2018). Disable that conversion before opening such files.

  • Files that mix tabs and spaces as delimiters need to be cleaned before loading.

Why did some columns not show up after upload?

If a numeric column contains a non-numeric character or a space, that column is dropped (or the upload errors). Clean these values before uploading.

Why can’t I see all the background data in Main Plots?

To keep plotting fast, only 10% of non-significant (NS) genes are drawn by default. For publication figures, open Main Options on the left and set Background Data (%) to 100%.

Why do I get an error when I click DE Genes in the Enrichment tab?

Enrichment needs the correct organism selected first. Choose it, set your other parameters, and click Submit. The enriched categories then appear on the Tables tab; select a category and click DE Genes to see the genes behind it.

How do I download selected data from Main Plots / QC Plots / Heatmaps?

Set Choose dataset to selected under Data Options on the left. A new field, The plot used in selection, appears — pick Main plot, Main Heatmap, or QC Heatmap. Then click Download Data, or open the Tables tab to view the selection.

How do I switch between light and dark mode?

Click the moon/sun button in the top-right of the navbar, or press T. The choice persists across the session. You can also jump between the six top-level tabs with the number keys 1–6 (shortcuts are ignored while you are typing in a field).

Can I save or share an analysis?

Yes. Click Bookmark (top-right) to capture the full analysis state behind a stable URL you can revisit or share. For a portable record, use the Export menu to download the session as an R script, R Markdown / HTML, a Jupyter notebook, or a ready-to-paste methods paragraph.

Is the AI assistant safe to use with sensitive data?

AI features are off by default and make no network calls until you enable them and choose a provider. For maximum privacy, use the local Ollama provider — the model runs entirely on your machine and no data leaves it. Even with a cloud provider, per-call privacy modes let you send only gene symbols, and API keys are stored in your OS keychain via keyring, never in plaintext.