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y.li.10
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Posts by y.li.1

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Comment: C: Why is batch effect correction an option in SCAN.UPC normalization?
... Thank you sincerely! And I appreciate your openness! Yunlei ...
written 6 months ago by y.li.10
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Comment: C: Why is batch effect correction an option in SCAN.UPC normalization?
... Hi Stephen! I've tried your approach (SCAN + UPC_Generic) but it produced a very bi-polarized distribution: only ~3% of the probesets are between 0.2 and 0.8. While UPC-transformed data has ~33% of the probesets in that range, which I thought is more reasonable. Another issue I had with UPC_Generic ...
written 6 months ago by y.li.10
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Comment: C: Why is batch effect correction an option in SCAN.UPC normalization?
... Ok! I'll follow your lead! Thank you so much! ...
written 6 months ago by y.li.10
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Comment: C: Why is batch effect correction an option in SCAN.UPC normalization?
... Thanks! My last question -- In your previous comment "if you first SCAN normalize the Affy data and then UPC transform those values using UPC_Generic", do you mean this is only for Affy data, and apply UPC_Generic alone for other data? And without batch correction, right? But again, you use differen ...
written 6 months ago by y.li.10
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Comment: C: Why is batch effect correction an option in SCAN.UPC normalization?
... I appreciate your advice very much! For now I'll settle down with UPC without batch adjustment, because UPC_generic requires extra information like lengths and GC content... Do you recommend to do post-normalization on the UPC-normalized values? I mean, first do UPC on every sample from any type of ...
written 6 months ago by y.li.10
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Comment: C: Why is batch effect correction an option in SCAN.UPC normalization?
... There're other types of microarray data. Not only Affymetrix. ...
written 6 months ago by y.li.10
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Comment: C: Why is batch effect correction an option in SCAN.UPC normalization?
... Hi Stephen, Thanks for your quick and elaborate answer! You answered all my questions! The only thing left is to decide whether to use batch information or not. What would you do? Would it still be a fair comparison if I normalize some datasets with batch information and some without? Thanks! Yun ...
written 6 months ago by y.li.10
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Why is batch effect correction an option in SCAN.UPC normalization?
... Hi, My goal is to normalized multiple GEO microarray datasets to make them comparable to each other and to future samples. I'm using UPC function in the SCAN.UPC package. I saw there's an option to provide batch information for each sample and the batch effect will be corrected. I read the followin ...
normalization scan.upc upc batch effect correction written 6 months ago by y.li.10 • updated 6 months ago by Stephen Piccolo530

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