Question: UPC correction for GC content?
0
gravatar for minnie
3.8 years ago by
minnie0
minnie0 wrote:

Hello,

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 pd.mogene.2.0.st 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?
0
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 pd.mogene.2.0.st automatically.

-Steve

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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