User: Dan Du

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Dan Du210
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Posts by Dan Du

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Job: Postdoctoral Scientific Researcher with a focus on bioinformatics in Rostock (Baltic Coast), Germany
... The Institute for Biostatistics and Informatics in Medicine and Ageing Research at the Rostock University Medical Center (Germany) seeks, pending budgetary approval, and starting July 1 or as soon as possible thereafter, and to be continued for up to 5 years, candidates for the position of a   Ful ...
jobs job bioinformatician job written 2.5 years ago by Dan Du210
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Comment: C: Faulty entry in org.Hs.eg.db, a force check perhaps?
... Hi Hans-Rudolf, Thanks for the example, I thought this might be the case, obviously have not been working with worms before. But good to know, so no simple way to check this then.  Case closed. Best, Dan ...
written 2.6 years ago by Dan Du210
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Comment: C: Faulty entry in org.Hs.eg.db, a force check perhaps?
... Hi Marc, Fair enough, I agree forcing a removal is kind of crossing the line here, this should be the job of NCBI. However I would still suggest at least issue a warning when certain keys returned by keys(x, keytypes='sometype') clearly violating the naming convention. Here is a small patch for Ann ...
written 2.6 years ago by Dan Du210
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Faulty entry in org.Hs.eg.db, a force check perhaps?
... Hi Marc and others, Recently a funny entry popup in org.Hs.eg.db during some internal mapping checkup, library(org.Hs.eg.db) select(org.Hs.eg.db, keys='16592263', columns=c('SYMBOL','ENTREZID'), keytype ='ENSEMBL') # ENSEMBL SYMBOL ENTREZID #1 16592263 RPL21P28 100131205 select(org.Hs.eg.db, ...
org.hs.eg.db written 2.6 years ago by Dan Du210
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Comment: C: reactome.db: reactome IDs not mapped to pathway names
... Super! the link works now! Will try it out! Thanks a lot! keep bugging... the name versioning seems odd,  should it not be 'reactome.db_1.52.0.tar.gz' instead of 'reactome.db_1.0.52.tar.gz', of coz which wont interfere with the installation. ...
written 2.6 years ago by Dan Du210
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Comment: C: reactome.db: reactome IDs not mapped to pathway names
... Hi Willem, glad to hear that a solution is in place.  btw, the link you posted gives a '404 not found', could you please check it again? ...
written 2.6 years ago by Dan Du210
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Answer: A: reactome.db: reactome IDs not mapped to pathway names
... Hi Johannes,  I got bitten by the same problem recently, currently I have to patch a little to catch those unmapped IDs.  Hopefully someone sees this... (it is not like you can now easily cc the maintainer like we were on mailing list...) cheers, Dan ...
written 3.0 years ago by Dan Du210
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Answer: A: Problem in generating heatmap after R and Bioconductor Update
... Hi Remo, There is a bug in the gplots version you are using (2.14.0), which has been fixed in 2.14.1, so run an update should fix your problem, you example works fine for me. > Release 2.14.1 - 2014-06-30 > --------------------------- > > Bug Fixes: > > - Correct bug in Colv dent ...
written 3.3 years ago by Dan Du210
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Answer: A: older version of org.Hs.eg.db
... Hi 1frcn, this one should be close enough, http://bioconductor.org/packages/2.7/data/annotation/html/org.Hs.eg.db .html with a time stamp "Packaged: 2010-10-04 18:33:30 UTC; mcarlson", while there is no guarantee that this will match to the one GeneTrail was using. Best, dan On Wed, 2014-04-16 at ...
written 3.6 years ago by Dan Du210
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Comment: C: Gviz: axes related parameters
... Hi Maxim, Perhaps you should read the package vignette more carefully given that you had indeed read it, say the first subsection of Track classes maybe. Since you had never shown us what you had done with any Gviz related codes. And regarding the cross which you think is important, someone correc ...
written 3.7 years ago by Dan Du210

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