I've come across many posts about common errors using GAGE, and many of these common pitfalls relate to mismatching ID systems (Entrez gene ID, gene symbol, etc). I've read the "Gene set and data preparation" vignette, but still get errors when I try to convert my gene symbols to Entrez IDs.
I have two questions:
1. Is there a way to map more "efficiently" gene symbols to Entrez IDs? For example, of 38720 unique input IDs, 8850 of my genes remain unmapped. I am using the mouse data set, trying to map gene symbols in my featureCounts output.
2. What does it really mean when I fail to download xml/png files for my GAGE analysis? I get errors like:
Info: Downloading xml files for hsammu04060, 1/1 pathways.. Warning: Download of hsammu04060 xml file failed! This pathway may not exist!
Thanks in advance.