Entering edit mode
2.5 years ago
asalimih
▴
60
Hello,
I have a candidate gene which I want to check if it is related to important pathways/gene-sets in a dataset that its samples are from one biological group (tumor samples). I came up with two methods:
- Projecting the expression matrix to gene-set space using ssGSEAProjection and then getting the correlation between my candidate gene expression and enrichment scores.
- Grouping samples into low and high expression groups based on the candidate gene and running a standard GSEA.
are these approaches correct? or is there any other method to do this properly?
To give more context, I chose this candidate from another dataset which had normal and tumor samples (using DEA and GSEA)
