For differential expression Group A vs Group B, genes that have a higher expression in group A compared to group B, should be listed with a positive fold change, and genes that have a lower expression in group A compared to group B should have a negative fold change.
For some differential expressions with the experimental setup All group pairs, the opposite is reported: Genes with higher expression in group A are reported with a negative fold change, for example -2.54 when it should be 2.54, while genes with lower expression in group A are reported with a positive fold change. The fold change absolute value is correct.
The issue does not impact the features listed in the Biological insights table (Canonical pathways, Upstream regulators and Diseases and functions). However, on the detailed Biological insights view, Prediction will be the opposite of what it should be (e.g. Activated instead of Inhibited).
Check the experimental setup setting for your experiment. It is listed in the Experimental summary and QC report. If your experiment was designed with the experimental setup Across groups (ANOVA-like) or Against control group, your differential expression results are not affected.
If your experiment was designed with experimental setup All group pairs, it may be affected. You can check if it is by comparing fold change values and heat map colors:
We recommend that you redo your affected experiments in RNA-seq Analysis Portal 3.0.1 or later version.
QIAGEN RNA-seq Analysis Portal 3.0 and earlier.
The issue was fixed with the release of RNA-seq Analysis Portal 3.0.1, November 2, 2022