User: Manhong Dai

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Manhong Dai200
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Posts by Manhong Dai

<prev • 20 results • page 2 of 2 • next >
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Answer: A: use alternative CDF in aroma.affymetrix in linux
... 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 Dai200
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Bioconductor Digest, Vol 65, Issue 23
... 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/ ...
cdf probe affy gcrma written 11.4 years ago by Manhong Dai200
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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 Dai200
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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 Dai200
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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 Dai200
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Bioconductor Digest, Vol 47, Issue 26
... 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 ...
go cdf probe affy gcrma process convert written 12.9 years ago by Manhong Dai200
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Bioconductor Digest, Vol 44, Issue 28
... 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 ...
cdf written 13.1 years ago by Manhong Dai200 • updated 13.1 years ago by Jenny Drnevich2.2k
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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 Dai200
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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 Dai200
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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 Dai200

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