Differential Expression Table shows max 10,000 genes

[gokulvk]

I uploaded a dataset that had data for 100,000 genes, but the final differential expression table only shows around 11,500 genes, and the expression matrix only shows data for 5000 genes. How can I see the data for every single gene that I gave to the program? Thanks!

[denis-torre]

Did you try downloading the expression matrix from the user dashboard? If so, how many rows does that file contain?

The observed difference is likely due to the fact that the uploaded data contains duplicate gene symbols and/or lowly expressed genes.

This is because BioJupies automatically filters datasets by (1) merging the expression of rows labeled with the same gene identifier, and (2) removing lowly expressed genes prior to performing differential gene expression.

If you are analyzing transcript-level data, labeling rows with unique transcript identifiers will prevent the counts from being collapsed to the gene level.