Question: UPC and Sequence file to remove GC bias
0
gravatar for sanj
4.6 years ago by
sanj20
United Kingdom
sanj20 wrote:

Hi,

 

I have been trying to use UPC_Generic_ExpressionSet function from the SCAN UPC package with Human Exon Array dataset and was stuck at a point. I want to use UPC based detection and correct for GC content but the sequence file for Affymetrix is at probe level whereas I am using alternative exon array mappings from BrainArray. Thus the expressionset contains SCAN normalised intensities at exon level. In this case do I need to supply information about sequence of each exon? If not then how should I approach this when using alternate mappings?

Thanks.

 

 

 

ADD COMMENTlink modified 4.6 years ago by Stephen Piccolo560 • written 4.6 years ago by sanj20
Answer: UPC and Sequence file to remove GC bias
0
gravatar for Stephen Piccolo
4.6 years ago by
United States
Stephen Piccolo560 wrote:

No, you shouldn't need to supply any sequence data. The CEL files contain the sequence for each probe and will perform the correction for nucleotide composition (including GC content). It will do this whether or not you are using BrainArray mappings. Please let me know if that doesn't answer your question.

ADD COMMENTlink written 4.6 years ago by Stephen Piccolo560

Thanks for the reply. When I used the UPC detection function with the Affymetrix platform the function runs through the iterations but each time it shows No correction will be made for GC content. That confused me a bit but I think that is probably because no argument is passed to the sequenceFeatureName. 

ADD REPLYlink written 4.6 years ago by sanj20

The output doesn't say that specifically, but it should be doing it. If you want, you can send me the code you are using, along with the output, and I can take a look.

ADD REPLYlink written 4.6 years ago by Stephen Piccolo560
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