[BioC] probe expression profile to gene expression profile

[Sean Davis]

Weiwei Shi wrote:
> Dear All:
>
> Here is a general question and I apologize if it is a little bit off
> topic (but I believe bioconductor must have some solution for that.)
>
> Is there a guideline or good tool to get "gene" expression profile
> from "probe" expression profile? In this process, I am concerned that
> such tool or guide should address the issues of "multiple probes to
> one gene" and "one probe to multiple genes".
>
>   
Don't deal with the first case.  Do all of your analyses at the probe 
level.  There probably is not a safe, totally general way to aggregate 
probes in a gene expression context.  Instead, do you differential 
expression testing and then map probes to genes for downstream 
processing (looking up in Pubmed, etc). 

The second case can't be dealt with appropriately without knowing why 
one probe maps to multiple genes.  In general, unless you do your own 
annotation (using blast, for example), it will be difficult to make a 
call in the general case.  However, in some cases, the answer is 
"obvious".  In the case you emailed about earlier today (one probe 
hitting 3 genes), it was fairly obvious what the answer was, since one 
of the genes was a "Refseq" gene while the other two were simply 
computationally predicted genes.  The most important point is to know 
what sources of annotation are being used, what their limitations are, 
and how they relate to other sources of annotation--this knowledge is 
often not easy to come by, but is invaluable.

> I believe it is a non-trivial process and automation  of this process
> might not be easy:
>   
Automation really isn't possible, since there is not a general solution 
to every case.  My rule of thumb is to maintain as much information as 
possible throughout the process of data analysis and then do some 
biologic knowledge curation when the gene lists are in.  Unfortunately, 
there really isn't a fantastic substitute for this last step.

Just my two-cents worth.

Sean