User: Yuk Fai Leung
Yuk Fai Leung • 100
- Reputation:
- 100
- Status:
- New User
- Location:
- Last seen:
- 14 years, 11 months ago
- Joined:
- 15 years, 2 months ago
- Email:
- y******@cgr.harvard.edu
Posts by Yuk Fai Leung
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... 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 ...
written 14.9 years ago by
Yuk Fai Leung • 100
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... 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 14.9 years ago by
Yuk Fai Leung • 100
• updated 14.9 years ago by
Jean Yee Hwa Yang • 920
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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 14.9 years ago by
Yuk Fai Leung • 100
0
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1
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... 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 14.9 years ago by
Yuk Fai Leung • 100
• updated 14.9 years ago by
Michael Benjamin • 120
0
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1
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... 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 14.9 years ago by
Yuk Fai Leung • 100
• updated 14.9 years ago by
Jean Yee Hwa Yang • 920
0
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1
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... 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 14.9 years ago by
Yuk Fai Leung • 100
• updated 14.9 years ago by
Jean Yee Hwa Yang • 920
0
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... 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 15.1 years ago by
Yuk Fai Leung • 100
0
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2
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554
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... 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 ...
written 15.1 years ago by
Yuk Fai Leung • 100
0
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1
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635
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1
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... 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 15.2 years ago by
Yuk Fai Leung • 100
• updated 15.2 years ago by
Ramon Diaz • 1.1k
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... 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 15.2 years ago by
Yuk Fai Leung • 100
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