User: Daren Tan

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Daren Tan120
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Posts by Daren Tan

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Gene symbol to KEGG gene ids
... Is Entrez ID = NCBI gene ID = KEGG ID ? On Fri, Apr 17, 2009 at 7:52 PM, Daniel Brewer wrote: > In the case of humans it seems that the KEGG ID equals the ncbi gene ID. > > Many thanks > > Dan > > michael watson (IAH-C) wrote: >> Hi Daniel >> >> Have a look a ...
written 10.6 years ago by Daren Tan120
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Comment: C: Visualise KEGG pathway and highlight genes
... This solution is exactly what I am looking for in my previous post. How to improve the resolution ? On Fri, Apr 17, 2009 at 6:29 PM, Paolo Sonego wrote: > Hi Daniel, > If you wish to convert the gif generated at the specific url (taking > advantage of the KEGGSOAP package) to a PDF then y ...
written 10.6 years ago by Daren Tan120
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Comment: C: Retrieving KEGG pathway diagrams via KEGGSOAP
... Grateful for the help. Now I can get some nice KEGG pictures. On hand, I have about 20 pathways for visualization, how can I download the 20 gifs or possibly higher resolution pictures and collate them into a pdf ? Possible to do all these steps via R ? On Fri, Apr 17, 2009 at 10:02 AM, Saroj K Moh ...
written 10.6 years ago by Daren Tan120
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Retrieving KEGG pathway diagrams via KEGGSOAP
... There was an earlier example about KEGGSOAP, which I am looking for all this while. My work centers around hsa, so I tried one of the pathway annotated in human and sound genes. However, NULL is always returned. What is wrong ? > get.genes.by.pathway("path:hsa03050") [1] "hsa:100132108" "hsa:10 ...
keggsoap written 10.6 years ago by Daren Tan120 • updated 10.6 years ago by Paolo Sonego140
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Example in SLqPCRdata package
... In one of the example in SLqPCRdata package stated below, I am unsure in the last line i.e. exprData <- normPCR(SLqPCRdata, c(3,4)), whether SLqPCRdata should have been relData ? According to the help page of normPCR, it requires a data.frame containing relative quantities. SLqPCRdata contains th ...
written 10.7 years ago by Daren Tan120
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Answer: A: ChrMapHyperGParams and linearMTest in Category
... Hope someone or the developer of GOStats/Category can answer my queries. On Sat, Apr 4, 2009 at 11:28 AM, Daren Tan wrote: > Beyond the scope of the manual and vigenettes of Category and GOStats, > I would like to understand more about ChrMapHyperGParams and > linearMTest. > > After ...
written 10.7 years ago by Daren Tan120
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Help me understand org.Hs.eg.db
... I am using two approaches to get EntrezID to genes mapping, as well as genes to EntrezID mappings. toTable gives same number of mappings in both directions, but mget doesn't. Which approach should I trust and why ? > dim(toTable(org.Hs.egSYMBOL2EG)) [1] 39824 2 > dim(toTable(org.Hs.egSYMB ...
go written 10.7 years ago by Daren Tan120 • updated 10.7 years ago by Hervé Pagès ♦♦ 14k
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ChrMapHyperGParams and linearMTest in Category
... Beyond the scope of the manual and vigenettes of Category and GOStats, I would like to understand more about ChrMapHyperGParams and linearMTest. After successfully using "GOHyperGParams" and "KEGGHyperGParams" with platform-independent annotation database "org.Hs.eg.db", I tried to do the same with ...
annotation gostats category written 10.7 years ago by Daren Tan120
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XPS vs APT
... I am migrating from affymetrix apt-probeset-summarize to XPS. How do I get expression values via XPS corresponding to the following apt-probeset-summarize options ? 1) "rma-bg,quant-norm.sketch=-1.usepm=true.bioc=true,pm-only,med- polish" 2) "quant-norm.sketch=-1.bioc=true,pm-only,plier" 3) "quant- ...
xps written 10.7 years ago by Daren Tan120 • updated 10.7 years ago by cstrato3.9k
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Limma: 2 venn diagrams on single page
... I would like to place 2 venn diagrams generated by limma on single page. However they are very squeezy and there are much empty space above and below them. The output is attached to this post. I would like to remove the empty space, so that the venn diagrams are as large as possible while retaining ...
hgu133a limma written 10.7 years ago by Daren Tan120 • updated 10.7 years ago by James W. MacDonald52k

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