User: Manhong Dai
Manhong Dai • 200
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- Last seen:
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- Joined:
- 13 years, 1 month ago
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Posts by Manhong Dai
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... Dear Shirley,
Thanks a lot for your interest in our custom CDF, you can go
to
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF
_download.asp#v11 and select link 'Click Me' for a custom CDF type,
then the last column of the huge table is what you want.
Best,
Manhong
...
written 11.0 years ago by
Manhong Dai • 200
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... Hi John,
Thanks a lot for your interest in our custom CDF. I think I
can answer some of your questions.
The place you download the tiling array custom CDF has a
mapping between original cdf name, and custom CDF name.
For example, at http://brainarray.mbni.med.umich.edu/ ...
written 11.4 years ago by
Manhong Dai • 200
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Answer:
A: inquiry for CDF file
... Hi Hyeong-Min,
Please google "custom CDF" and go to version 11. We released
ENTREZG
custom CDF for almost all affymetrix chips.
We didn't put them in bioconductor repository yet, because we
are still
struggling with other custom CDF types.
Best,
Manhong
>Hello.
>I'm look ...
written 11.4 years ago by
Manhong Dai • 200
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Comment:
C: MBNI custom CDF packages
... Hi Henrik,
Thanks a lot for this excellent suggestion. Especially the
sample code
would help. I would try to use binary in version 11 of custom CDF.
Best,
Manhong
On Tue, 2008-05-27 at 07:43 -0700, Henrik Bengtsson wrote:
> Hi Manhong,
>
> thanks for doing this big job. In you p ...
written 11.5 years ago by
Manhong Dai • 200
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Answer:
A: MBNI custom CDF packages
... Hi Burak,
Thanks a lot for your interest in our custom CDF.
I am working hard on version 11, because this time we planed
to support
almost all Affymetrix chips and some kinds of one-mismatch probe
sequence alignment. The data I am processing is at Tera-byte level.
I exp ...
written 11.5 years ago by
Manhong Dai • 200
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... Hi Paul,
This error message shows up because the R session needs to
load an
package for each chip. The package included two function i2xy and
xy2i,
which can convert probe coordinate to an integer and vice versa.
Because you are using two chips in one session. When the
second packa ...
written 12.9 years ago by
Manhong Dai • 200
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... Hi Dana,
We ever released an R package that can remove probes from cdf
environment, which is at
http://arrayanalysis.mbni.med.umich.edu/MBNIUM.html#ProbeFilter
Some peoples have tested it and it seems there is no glitch.
Best,
Manhong Dai
> Hello,
> I am trying to remove in ...
written 13.1 years ago by
Manhong Dai • 200
• updated
13.1 years ago by
Jenny Drnevich • 2.2k
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Comment:
C: hs133phsentrezg metadata
... Hi Jim,
It is always inaccurate to assign one or multiple chromosome
locations
to each probeset for either Affy's original cdf or our custom CDFs.
We know a probeset's genome location should be calculated from
its
probes' genome location, and it should be a range or multiple ranges ...
written 13.1 years ago by
Manhong Dai • 200
0
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Comment:
C: hs133phsentrezg metadata
... Hi Jim,
In our custom cdf, some hits<1 probes would be used. For
example, when
a probe has a hit with an allele of a snp, and the snp's another
allele
has hits=1 match with genome, although the probe has no hit with
genome
at all, we would use this probe and its genome location as a cand ...
written 13.2 years ago by
Manhong Dai • 200
0
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Answer:
A: hs133phsentrezg metadata
... Hi An,
Our custom CDF annotation package has only gene name for each
probeset
because we designed it this way.
A probeset's probes could have matches on different location
or
chromosomes, even some probes have no match on genome at all, but they
belong to this probeset because they ...
written 13.2 years ago by
Manhong Dai • 200
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