Suggestion for enrichment analysis for small microarray set.

[zhen-fu]

I am working on a microarray dataset that has 860 genes in total. I did DE gene expression analysis, there were 60 up regulated genes and 80 down-regulated genes.

I would like to do enrichment analysis. Would it appropriate to use over-representation analysis (ORA), or even gene set enrichment analysis (GSEA)? My concern is the 860 gene microarray is a much reduced gene set compared to whole transcriptome, and it might introduce bias. Any comments are welcome!

[huerqiang]

In this case, the ORA algorithm is suitable.