User: Stephen Piccolo

gravatar for Stephen Piccolo
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Posts by Stephen Piccolo

<prev • 108 results • page 1 of 11 • next >
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Comment: C: Why is batch effect correction an option in SCAN.UPC normalization?
... Hi Yunlei, 1. Although UPC-transformed data with ~33% in the middle range may be more reasonable, the UPC method provides a more bimodal distribution for other data types (due to the underlying distributions of these other data types as well as assumptions we make). That's why I suggested to do it ...
written 12 weeks ago by Stephen Piccolo530
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Comment: C: Why is batch effect correction an option in SCAN.UPC normalization?
... Yes and yes. ...
written 12 weeks ago by Stephen Piccolo530
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Comment: C: Why is batch effect correction an option in SCAN.UPC normalization?
... Lengths and GC content are optional. UPC_Generic should just accept the expression values so should be easy to apply, but let me know if you find otherwise. In theory you shouldn't need to do post-normalization on UPC-normalized values. However, realistically, there will still be some systematic di ...
written 12 weeks ago by Stephen Piccolo530
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Comment: C: Why is batch effect correction an option in SCAN.UPC normalization?
... In that case, I would say not to use batch adjustment because, as you say, it would be inconsistent to use it in one place rather than another. However, one limitation of the UPC method is that the shape of the data is pretty different for UPC normalized Affymetrix data compared to UPC normalized da ...
written 12 weeks ago by Stephen Piccolo530
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Comment: C: Why is batch effect correction an option in SCAN.UPC normalization?
... Are you combining it with other type of microarray data or RNA-seq data? Or will it all be Affymetrix data? ...
written 3 months ago by Stephen Piccolo530
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Answer: A: Why is batch effect correction an option in SCAN.UPC normalization?
... Thanks for your question and sorry for the confusion. I put an option to do batch normalization in SCAN.UPC, but most people don't use it. I did this before the sva package was available. Now I would just point people to the sva package. First, I'll answer your questions: 1. Yes, that's a key aspe ...
written 3 months ago by Stephen Piccolo530
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Comment: C: Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
... Thanks for the detailed response. There's no reason that SCAN.UPC can't handle these conventional transcript-level mappings. I haven't come across anyone who needed this, though. Have you? ...
written 10 months ago by Stephen Piccolo530
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Comment: C: Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
... Here's a link to the BrainArray site: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp#v22 ...
written 10 months ago by Stephen Piccolo530
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Answer: A: Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
... I apologize for my delay in replying. I may be misunderstanding what you want to do, but you should be able to solve this by using BrainArray annotations. You can read about this in the SCAN.UPC vignette. BrainArray now has annotations for the HTA 2.0 arrays. You can use the probeSummaryPackage arg ...
written 10 months ago by Stephen Piccolo530
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Comment: C: Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
... I will have to go into the code to remember why that is the case and see if there is a better way to handle it. It might take me a few days (due to the US holidays) to get to it. Does hta20transcriptcluster.db have probe information? ...
written 10 months ago by Stephen Piccolo530

Latest awards to Stephen Piccolo

Popular Question 20 months ago, created a question with more than 1,000 views. For Filtering pmSequence based on probe target level for HTA 2.0 arrays
Centurion 20 months ago, created 100 posts.
Scholar 21 months ago, created an answer that has been accepted. For A: normalization with mas5
Scholar 3.4 years ago, created an answer that has been accepted. For A: normalization with mas5
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Can I feed TCGA normalized count data to EdgeR for differential gene expression

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