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Map Probe Set Expression To Gene

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

mapping expression
• 3,447 views • link
updated by B. Arman Aksoy B. Arman Aksoy • written by dcolinmorgan dcolinmorgan

1 answer

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
• 151 views • link
written by B. Arman Aksoy B. Arman Aksoy

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

• 0 views • link
written by dcolinmorgan dcolinmorgan

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