User: John Zhang

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John Zhang2.9k
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Posts by John Zhang

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CSHL course
... Hi, Vince, Tracy told me that you would like to know if I can go this summer for the CSHL course. I can try to go for the first weekend when the course begings (I guess that is when you need more help). I tried to do so last year but something upexpected happed. Jianhua ...
go written 10.3 years ago by John Zhang2.9k
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Answer: A: Annotation package for Yeast Genome S98 array ?
... > >I am just wondering if there is any annotation package for the affymetrix >Yeast Genome S98 array ? If so, could anyone please give me the name of it. >source("http://www.bioconductor.org/biocLite.R") >biocLite("ygs98") will have the package installed. > >Many thanks. > ...
written 11.7 years ago by John Zhang2.9k
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Answer: A: RdbiPgSQL: slowness in dbWriteTable
... > >Yup, your method is essentially what I came across yesterday afternoon, >with some slight variations. What you outline is a bit better >though. This works for my immediate task, although I'm going to need a >way to allow this to be automated (hopefully within RdbiPgSQL >itsel ...
written 11.8 years ago by John Zhang2.9k
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Answer: A: how to convert gene identifier to symbol?
... > > I am using library hgu95av2 to generate a list of pathways > >xx <- as.list(hgu95av2PATH2PROBE) > However the results are gene identifiers. > > > xx[2] > $`00642` > [1] "38377_at" "840_at" "31873_at" "40782_at" "35004_at" > [6] "35203_at" "39238 ...
written 11.8 years ago by John Zhang2.9k
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Answer: A: AnnBuilder questions
... > >I tried to check the library, everything worked well >except the following error : > >Problem number 1 : > >'yeastAgilentLOCUSID' is deprecated >rather use 'yeastAgilentENTREZID' >see help("Deprecated") This applies to packages containing an Entrez gene id environment ...
written 11.8 years ago by John Zhang2.9k
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Answer: A: KEGGSOAP: color.pathway.by.objects
... > >However, the "color.pathway.by.objects" does not seem to work (at least the way I am thinking it should). Specifically, the colors for "fg.color.list" and "bg.color.list" stay the same no matter what color I put in there. I can see no difference in the pathway that is generated. KEGGSOAP ...
written 11.8 years ago by John Zhang2.9k
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Answer: A: AnnBuilder problem with custom List of genes
... > > >I am trying to build up an annotation package for an old chips for which there is no annotation in BioC. I'am looking for AnnBuilder. First I create a file GEM.txt, with two columns, the first corresponds to probe location on the array (univocal numbers); the second corresponding to g ...
written 11.8 years ago by John Zhang2.9k
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Answer: A: KEGG package
... > >I would like to use GSEA to analyze customed microarrays. I need to map genes from ACC number to KEGG pathways. How can I do it using KEGG package? I could not find any documents for KEGG package. Is there any example? Try the following in R to see if there is anything helpfull: >KEG ...
written 11.9 years ago by John Zhang2.9k
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Answer: A: Getting all the gene names and the locus link ID from different platforms
... > >I am trying to get ALL the gene names (symbol) and their corresponding locus >link ID from around 10 different Affymetrix platforms, but I am not quite >sure how to do that.....effeciently. > >I know I could use the aafSymbol from the annaffy package or the getLL / >getSYMBO ...
written 11.9 years ago by John Zhang2.9k
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Answer: A: Affymetrix annotation package
... >> >> Is "HG919-HT919" really an accession number? I do not get any hits at NCBI's GenBank. NetAffx gives the same identifier for that probeset, but in a field called "Representative Public ID". >> There are some more probesets with "HGXXX-HTXXX" as ACCNUM on the hgu95av2 chip. Wh ...
written 11.9 years ago by John Zhang2.9k

Latest awards to John Zhang

Popular Question 8.9 years ago, created a question with more than 1,000 views. For RE: Bioconductor web page
Centurion 8.9 years ago, created 100 posts.

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