Question: How to define the gene value if a gene is represented by multiple probe sets
1
gravatar for zero_hsy
4.0 years ago by
zero_hsy90
China
zero_hsy90 wrote:

Hello:

     I was doing .cel.And when I mapped the probe id to gene symbol, I found sometimes a gene is represented by multiple probe sets. How to define this gene value?

gene value probe id cel • 1.1k views
ADD COMMENTlink modified 4.0 years ago by Irsan6.8k • written 4.0 years ago by zero_hsy90
1

+1. In my opinion this question has received surprisingly little attention, especially considering that different probes on the same gene might show very different patterns of expression. I vaguely remember a paper suggesting that the best way to represent the whole expression of a gene is to use the the probe with the highest intensity (can't find the ref just now...).

ADD REPLYlink written 4.0 years ago by dariober10.0k
9 out of 10 times the probe with the highest signal is the 3'-end probe forum reasons I explained in my answer below.
ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Irsan6.8k
2
gravatar for Irsan
4.0 years ago by
Irsan6.8k
Amsterdam
Irsan6.8k wrote:
I suppose you are referring to gene expression arrays that can have multiple probes per gene. If you want to have a single value you should take the probe closest to the 3'-end of the gene (so the end of the gene). This is because RNA molecules get degraded from the start of the molecule and therefore the signal/probe at the end of the molecule is most reliable. The reason why multiple probes were designed per gene was to quantify the extent of RNA degradation and to allow for differential isoform expression analysis.
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Irsan6.8k
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