User: Park, Richard
Park, Richard • 220
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- Last seen:
- 15 years ago
- Joined:
- 16 years, 5 months ago
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... Hi Andrea,
I have spent sometime trying to create microarray analysis interfaces
between visual basic to R/S-plus/ArrayAnalyzer. What types of
platforms were you thinking of using to implement this idea? I have
found that creating interfaces in s-plus is sort of cumbersome and
hard to adapt for mult ...
written 16.0 years ago by
Park, Richard • 220
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... Hi Everyone,
I was just talking with my PI the other day and he told me that he had
an interesting conversation with one of the lead developers at
affymetrix. I know there have been discussions about affy's move
toward a binary format and how this will affect open source
environments such as biocond ...
written 16.1 years ago by
Park, Richard • 220
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Answer:
A: Re: location in chromosome
... hi,
you should take a look at the annotate() package.
chromLoc-class Class chromLoc, a class for describing the location of
a gene on a chromosome.
chromLocation-class Class chromLocation, a class for describing genes
and their chromosome mappings.
I haven't dealt much with chromosome locations, I ...
written 16.2 years ago by
Park, Richard • 220
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... These are my two cents to the question. I would at first normalize
everything together via rma, which does poses risks of diminishing or
enhancing treatment effects. But I believe this would allow you to see
the overall picture of the data and give you a general sense of how
each treatment compares ...
written 16.2 years ago by
Park, Richard • 220
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Answer:
A: chips A,B and C
... Hi Nicolas,
Yes, I agree with Jim, since the 3 chips are testing different sets of
genes, it is not necessarily that important to normalize everything
together, since expression values in microarrray's are relative. But I
can see the need of normalizing everything together if you are trying
to link ...
written 16.2 years ago by
Park, Richard • 220
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... Hi Rafael,
I was just wondering if you could give me your opinion on my method of
normalization. I was always under the impression that it is best to
always renormalize the entire data set whenever you add or remove an
additional chip. This would correspond to your 0 method. I do
understand that thi ...
written 16.2 years ago by
Park, Richard • 220
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... Dear Adai,
I can not tell you what is the correct way of doing analysis, but
maybe I can give you a little insight by telling you how I do analysis
on my own chips. I am computational biologist and I have been doing
most of my labs microarray analysis for the past year.
We use affymetrix chips in o ...
written 16.2 years ago by
Park, Richard • 220
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... Hello everyone,
I was wondering if anyone knew of a function within bioconductor or
method to provide some sort of metric for replicate quality analysis.
I have typically been using multipanel graphs (having each replicate
plotted vs each other) to get a sense of the replicate qualities.
However, I ...
written 16.2 years ago by
Park, Richard • 220
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... Hi Everyone,
I am currently using the mt.teststat to calculate p-values between
various samples. I was wondering if anyone knew if it was ok to run
p-values on logged or non-logged values? In the past using MAS
processing, I always calculated pvalues on the raw values, however I
have recently switch ...
written 16.3 years ago by
Park, Richard • 220
• updated
16.3 years ago by
James W. MacDonald ♦ 50k
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... Dear Everyone,
Could someone please point me to the function within Bioconductor that
allows me to see the individual expression values for each of the
probes on a chip? I have a specific probe I want to look at and I
would like to see the 12-20 perfect match and mismatch pairs for that
probe id.
T ...
written 16.3 years ago by
Park, Richard • 220
• updated
16.3 years ago by
Laurent Gautier • 2.2k
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For P values on Log or Non-Log Values
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