User: Yuk Fai Leung

gravatar for Yuk Fai Leung
Yuk Fai Leung100
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13 years, 12 months ago
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14 years, 3 months ago
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y******@cgr.harvard.edu

Posts by Yuk Fai Leung

<prev • 10 results • page 1 of 1 • next >
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Affy analysis
... Hi, I am going to do affy analysis for the first time. After reading the previous related postings, I have some questions: 1. If I use the RMA method to estimate the true intensities, should I neglect the present call/absent calls? 2. If I should neglect the present/absent calls, is there any othe ...
normalization affy affycomp written 14.0 years ago by Yuk Fai Leung100
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combine two objects & adding/deleting arrays in an obj ect
... Thanks! But how about adding one/more experiments to an existing marrayRaw object? Fai ________ Yuk Fai Leung Bauer Center for Genomics Research Harvard University 7 Divinity Avenue Cambridge, MA 02138 Tel: 617-496-7134 Fax: 617-495-2196 email: yfleung@cgr.harvard.edu; yfleung@genomicshome.com URL: ...
written 14.0 years ago by Yuk Fai Leung100 • updated 14.0 years ago by Jean Yee Hwa Yang920
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Answer: A: bioconductor
... I would love to see a comprehensive manual like that. It would be very helpful for biologists. And I believe it is better to disseminate this manual online rather than as a printed text. Before this, it would be nice to have a vignette that contains a flowchart of a typical microarray analysis step ...
written 14.0 years ago by Yuk Fai Leung100
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RE: Bioconductor Digest, Vol 9, Issue 28
... I would love to see a comprehensive manual like that. It would be very helpful for biologists. And I believe it is better to disseminate this manual online rather than as a printed text. Before this, it would be nice to have a vignette that contains a flowchart of a typical microarray analysis step ...
microarray limma written 14.0 years ago by Yuk Fai Leung100 • updated 14.0 years ago by Michael Benjamin120
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combine two objects & adding/deleting arrays in an object
... Hi, Sorry for asking a simple question but I cannot find the answer in the archives. I want to know how to 1. Combine two objects of the same class, for example two marrayRaw objects. 2. Add/delete an array/experiment from a marrayRaw/marrayNorm object. Thanks in advance! Best regards, ...
written 14.0 years ago by Yuk Fai Leung100 • updated 14.0 years ago by Jean Yee Hwa Yang920
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Difference between the analysis of cDNA, spotted oligo arrays and comparative genomics hybridization?
... Hi there, Is it suitable to use the libraries for cDNA analysis (e.g. marrayNorm, marrayPlots, marrayTools) to perform low level analysis on spotted oligo arrays (e.g. MWG, Qiagen) or comparative genomics hybridization data? Thanks! Fai ________ Yuk Fai Leung Bauer Center for Genomics Research Har ...
written 14.0 years ago by Yuk Fai Leung100 • updated 14.0 years ago by Jean Yee Hwa Yang920
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Answer: A: Help on factorial experiment analysis using limma
... Dear Gordon, Thanks a lot for your prompt reply. I have more questions. > This is a saturated direct design for a two-way factorial experiment. > Good. Is it still ok to use limma to analyze the data if one or both diagonal experiment arrow is missing? I just realize I have another experime ...
written 14.2 years ago by Yuk Fai Leung100
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Help on factorial experiment analysis using limma
... Hi there, I have an experiment that looks like factorial experiment and I want to give it a try to use limma for its analysis. And I have a few questions The experimental scheme looks like this: 0: not-treated with the respective factor a: treated by factor a b: treated by factor b ab: treated by ...
limma written 14.2 years ago by Yuk Fai Leung100
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Simple questions about p values adjustment in limma/multt est
... Hi, Is the FDR assumed to be a certain percent (e.g. 5%) in the FDR adjustment for p values? If so, is it possible to change it? Are these FDR adjusted p-values the same as/similar to q-values in SAM procedure? Thanks in advance! Best regards, Fai ________ Yuk Fai Leung Bauer Center for Genomics ...
written 14.3 years ago by Yuk Fai Leung100 • updated 14.3 years ago by Ramon Diaz1.1k
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Answer: A: Defining Weights in marrayNorm.
... Hi there, I have encountered the same problem of using different weights to normalize my data recently. As a na?ve biologist with limited programming skills, I modified the maNormMain, maNormLoess and maNormMAD in a "dirty way" so that I may use the respective weights for each array. maNormMain & ...
written 14.3 years ago by Yuk Fai Leung100

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