Question: How to handle the problem of one probe set ID mapping to several genes in HG-U133 plus 2?
1
gravatar for mgab
4.3 years ago by
mgab50
Germany
mgab50 wrote:

Hi all. I am using HG-U133 PLUS 2  platform. I am having one problem of one  probe set ID mapping to several genes? How can one resolve this problem? is there a bioconductor software that deals with this problem? Thank you.

microarray • 1.4k views
ADD COMMENTlink modified 4.3 years ago by poisonAlien2.8k • written 4.3 years ago by mgab50
1
gravatar for Chris Evelo
4.3 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

Yes there is. The common way to solve this is to use alternative probeset annotations. These are available as custom .cdf files from the brain array website. These custom cdf files solve a number of other problems with bad probes too.  

One easy way to use these is via our arrayanalysis.org service that allows you to do quality control, normalisation, statistical modelling and pathway analysis using these custom ,cdf files if you select these.

 

ADD COMMENTlink written 4.3 years ago by Chris Evelo10.0k

Thanks Chris. I will use this software. Excellent.

ADD REPLYlink written 4.3 years ago by mgab50
0
gravatar for poisonAlien
4.3 years ago by
poisonAlien2.8k
Asgard
poisonAlien2.8k wrote:

One way is to take the mean value of all the probesets mapping to same genes (but its not recommended for so many obvious reasons). 

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by poisonAlien2.8k

Oops. Sorry, I read your question wrong. 

ADD REPLYlink written 4.3 years ago by poisonAlien2.8k
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