Question

UPC and Sequence file to remove GC bias

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sanj ▴ 20

@sanj-5889

Last seen 8.3 years ago

United Kingdom

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.

UPC_Generic_ExpressionSet brainarray • 1.7k views

ADD COMMENT • link updated 9.7 years ago by Stephen Piccolo ▴ 600 • written 9.7 years ago by sanj ▴ 20

score 0 · Answer 1 · 2015-04-07

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Stephen Piccolo ▴ 600

@stephen-piccolo-6761

Last seen 4.3 years ago

United States

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 COMMENT • link 9.7 years ago Stephen Piccolo ▴ 600

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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 REPLY • link 9.7 years ago sanj ▴ 20

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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 REPLY • link 9.7 years ago Stephen Piccolo ▴ 600