Question: UPC correction for GC content?
gravatar for minnie
3.8 years ago by
minnie0 wrote:


I am trying to use the UPC_Generic_ExpressionSet function on an expressionset (based on mouse Affymetrix data) and had trouble adjusting for the GC content bias. I know in the manual it says one can specify in the sequenceFeatureName to account for the GC content, but I wanted to ask how I may go about specifying this? (I am not able to find any information on the sequence from our ExpressionSet object's metadata?).

The array I am working with is Mouse Affymetrix Gene 2.0 ST. Is there a way to use information from or an annotation file (not sure) to obtain the probe DNA sequence to adjust for the GC content? 

Any help/suggestions would be appreciated and hope I provided enough information as this is what I know as of now.

Thank you! - Min 




ADD COMMENTlink modified 3.8 years ago by Stephen Piccolo560 • written 3.8 years ago by minnie0
Answer: UPC correction for GC content?
gravatar for Stephen Piccolo
3.8 years ago by
United States
Stephen Piccolo560 wrote:

Hi Min,

Thanks for your question. I would recommend that you use the UPC() function rather than UPC_Generic_ExpressionSet() for this. The UPC() function is designed specifically for Affymetrix data. It should pull annotations from automatically.


ADD COMMENTlink written 3.8 years ago by Stephen Piccolo560

Hi Steve,

Thank you very much for the prompt reply! I have used the UPC() function on the cel files and it has worked nicely using the annotation from pd.mogene.2.0st .

Thank you again, Min

ADD REPLYlink written 3.8 years ago by minnie0
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