I am using GFOLD to select candidate enriched transcripts from an RNA-seq experiment. Treatment #1 contains two replicates while treatment #2 is a singleton. This produced some unexpected results in which a minor subset of genes have a RPKM greater in treatment #1 than treatment#2 yet the GFOLD value and the log2fdc values predict an enrichment in treatment #2.
Should the GFOLD predictions be prioritized over the RPKM values?
Does the GFOLD value just refer to the likelihood of the fold change?
I am having trouble understanding the limited information in the GFOLD manual.
Should the GFOLD predictions be prioritized over the RPKM values?
Does the GFOLD value just refer to the likelihood of the fold change?
I am having trouble understanding the limited information in the GFOLD manual.