I am currently looking at existing differential gene expression data another lab has uploaded to GEO (GSE48761). I have a few issues I don't know how to deal with:
1. How to salvage gene of interest data when one probe grabs multiple genes?
For example, I'm interested on the expression of a gene called TMSB4X. However, the only probe mapping to TMSB4X is the following:
How can I analyze expression of TMSB4X if the probe is catching all these other genes as well?
2. How to do statistics on gene expression when so many probes are grabbing multiple genes?
I am trying to build a contingency table looking at the differential gene expression of a family of genes within this dataset. However, in order to do this part of my contingency table needs to be 'every gene expressed in Werner's syndrome that isn't differentially expressed in Werner's syndrome and isn't one of my genes of interest' but again many of these genes are mapped to probes that contain multiple genes. How do I deal with this problem?
Happy to clarify anything