How to merge probes with the same gene symbol in soft file?

Question

[niutster]

Hi all,

I have downloaded from GEO one soft file and extracted some specified GSMs . The GSMs soft files were categorized based on probes names but when i mapped probes to genes symbol, i have understand some probes mapped to one gene symbol. How can i merge these probes and have unique gene symbols?

Answer 1

[mbens]

There is no general rule on how to deal with such probe sets in microarray data. Different probes mapping to the same gene symbol might correspond to different isoforms of that genes and are meaningful to analyse separately. Other probes might be prone to cross-hybridization and should probably be removed from the analysis.

For instance, you could concentrate your analysis on probes that vary the most across different condition. You could also take the median for each probe set (might be less prone to outlier caused by strong signals from cross-hybridization probes than the mean).