Before you start, obtain the complete upstream differential-expression table and its methods: organism, identifier type, numerator, denominator, model, adjustment method and shrinkage where known.
1. Import the complete results table#
On Add data → Count / DE tables, choose Import differential-expression results. A supported gene-ID column, log2FoldChange and an adjusted-p column are required. The importer checks the complete table, including safe unique identifiers, numeric ranges and supplied statistic direction.
2. Confirm the source direction#
Confirm the numerator and denominator used by the upstream software. Positive log2 fold change means higher expression in that numerator. Local contrast controls do not reverse or reinterpret an imported table.
| Setting | What it changes | When to change it / example |
|---|---|---|
| Source numerator / denominator | Determines how up and down are described. | Illustration: treated/control with +1 means a twofold higher expression ratio in treated. Reversing the comparison changes the sign. |
| Upstream method metadata | Controls what the report can truthfully attribute to the source analysis. | Leave an unknown p-adjustment method unknown; do not label it Benjamini–Hochberg by assumption. |
| alpha and |log2FC| | Selects direction-split gene lists from the supplied values. | A stricter alpha can reduce selected genes without refitting the upstream model. |
| Organism / identifier namespace | Controls downstream gene mapping. | A table of symbols needs compatible annotation settings; choosing a species cannot translate an unrelated ID namespace automatically. |
3. Preserve and check the import#
The project copy is bound to its SHA-256, size, row count and schema. Keep that copy intact; changes require renewed validation. Review applicable enrichment, figures and network outputs after running.
What can be produced#
Applicable outputs include volcano and p-value views, an MA view when the required mean-expression information exists, enrichment, STRING networks, set overlap and a preranked .rnk file. Imported ranking uses confirmed log2FoldChange rather than an upstream statistic of undocumented scale.
Troubleshooting: the statistic sign is rejected
Check the upstream export and column alignment. A shifted delimiter can put unrelated numbers into the statistic column. Do not flip a statistic merely to pass import; establish its definition and source direction first.