Map Probe Set Expression To Gene

Question

[dcolinmorgan]

I'm trying to debug and test a drug repositioning tool and need to find a (simple) way to map probe set expression to the gene level, presumably by averaging expression over redundant/overlapping probe sets to represent gene expression

I found this but am not proficient enough in bioconductor/R to make any sense of it :

https://stat.ethz.ch/pipermail/bioconductor/2011-January/037195.html

Hoping for a simple workaround, maybe an excel plugin to accompany BRBtools output

Answer 1

[B. Arman Aksoy]

You can use GENE-E to accomplish this. Basically, you need to:

1. Load your probe-level data to GENE-E
2. Annotate your probes (your rows) with your probe to gene file (most of the time you can find these files on GEO)
3. Collapse your probe-level data to gene-level by grouping your rows
4. Export data or use built-in analysis tools

[dcolinmorgan]

this worked brilliantly - thank you for the quick, clear and concise help!