Probes - to - genes expression analysis question

Question

[landscape95]

Why do people often map probes to genes names when we do analysis based on expression matrix? is it ok if we do the analysis such as subtyping cancer type based on probes? Thank you!

[Jean-Karim Heriche]

The reason people map probes to genes is because this allows to do further analysis to gain biological insight e.g. what pathway is affected. Another aspect is that mapping probes to genes provides dimensionality reduction. If you don't care about these aspects, you could use the probes as variables in your analysis although you would probably still have to deal with the high correlation between probes targeting the same transcripts.

[boczniak767]

Probe-level analysis allows you to use it later, in case your probe-gene annotation improves.

you could use the probes as variables in your analysis although you would probably still have to deal with the high correlation between probes targeting the same transcripts.

Its true, but it also allows one to compare if probes targeting the same transcript shows coherent changes of expression of target genes.