I got confused to interpret the result derived by single sample gene set enrichment analysis.
To be specific, I have the expression data for a specific pathway and show it in a heatmap by log and z-score transformation of the FPKM matrix for each gene. See the heatmap as the following:
I further compressed the signature into a single score per sample by ssgsea algorithm using GSVA R package. by the following command:
enrichscore.meta <- gsva(as.matrix(FPKM.HUGO),meta.sig,method="gsva")
The enrichment score was then z-score and truncated to [-1,1], and shown in a scoremap. See the scoremap as the following:
You could see in the heatmap, under the first red subtype, there are two blocks with either upregulated (red rectangle) or downregulated (blue rectangle) expression, and the number of these dysregulated genes is almost 50-50.
However, how could I get a corresponding scoremap with totally blue score in the first subtype (black rectangle) which means this subtype is generally downregulated in this pathway (signature), as compared to other subtypes presented with relative high scores. It doesn't make any sense.
Is there anything wrong, and I hope to get some advises.
Many thanks advanced!