Question: which Agilent annotation db?
0
gravatar for Frederico Moraes Ferreira
4.3 years ago by
Brazil

Hi there, 

I need to map probes to genes, but not sure which mouse Agilent annotation data base to pick. Possible options are mgug4104a, mgug4120a, mgug4121a, mgug4122a. The experiment was performed with the following SurePrint G3 Mouse GE 8x60K Microarray Kit - G4852A. However, I could not find the chip model into the txt files. Could someone give me a clue? 

Best.

annotation agilent • 1.7k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Frederico Moraes Ferreira100
Answer: which Agilent annotation db?
0
gravatar for Axel Klenk
4.3 years ago by
Axel Klenk930
Switzerland
Axel Klenk930 wrote:

Dear Frederico,

try MmAgilentDesign026655.db

I *think* it'll provide mappings for the protein-coding genes but

not the lncRNAs and some controls.

Otherwise you'll have to download original annotation files from

Agilent's website and create your annotation database using the

AnnotationForge package which is a lot easier than it sounds...

Cheers.

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Axel Klenk930
Answer: which Agilent annotation db?
0
gravatar for Frederico Moraes Ferreira
4.3 years ago by
Brazil

Dear Axel, 

Thanks for replay. It seems there isn't a specific database for the Agilent kit that.  So, I have been using the mouse whole genome database mgug4122a. However, I was able to map about 20% of the probes only. I was wondering if perhaps I can map more probes with a different database.  

ADD COMMENTlink written 4.3 years ago by Frederico Moraes Ferreira100
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