Hello,
Can I perform a pathway enrichment study on z-scores by fgsea/GSVA package?
Say, if I have 4 samples from the same condition, but collected from different locations. And I want to check for the pathways enriched in each of these 4 samples.
Converting read_counts into z-scores, and then performing a pathway enrichment study on these z-scores, will be right?
Or we need log2FC values only for performing an enrichment study?
•
written
by
glady
1 answer
I guess you could do this, but I'd consider the statistics behind it meaningless given that you're violating a whole bunch of assumptions of GSEA analysis, e.g. replicates, a proper ranking statistic, etc. I'd just use ssGSEA instead, that at least gives you relative scores within a sample that are kind of comparable.
Log in to answer this question.
-
Correct way of doing enrichment analysis (ORA)
written by carolofharvest •
-
Is it valid to compare fold enrichment values from separate ORA runs across conditions
written by carolofharvest •
-
Combining microarray expression data
written by SnehaS •
-
GSVA analysis to comparison
written by psundar2 •
-
Forum: Tools to check if the user defined pathway is enriched in the data
written by Aynur •
-
Tutorial: Gene Set Enrichment Analysis
written by Hamid Ghaedi
-
GSVA and SSGSEA for RNA-Seq TPM data
written by young_bioinformatician
-
Pathway Enrichment on lncRNAs
written by glady
-
Pathway analysis and Gene enrichment Analysis Queries
written by bioinforesearchquestions
-
Interpreting Chip Seq Results
written by benjyrolls
