User: zhao shilin

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zhao shilin60
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3 years, 8 months ago
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5 years, 4 months ago
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Posts by zhao shilin

<prev • 6 results • page 1 of 1 • next >
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Re: KEGGprofile: "Error in phyper - Non-numeric argument to mathematical function" when using non model organism
... Dear Stefano, I've tested species Pseudovibrio FO-BEG1 ("psf" in KEGG database) and found it was imported into KEGG database in 2013 ( http://www.genome.jp/kegg-bin/show_organism?org=psf). But KEGG.db package was updated until 2012. I think that is the reason for the error message. Now I provide a ...
organism keggprofile written 3.7 years ago by zhao shilin60
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Answer: A: KEGGprofile: "Error in phyper - Non-numeric argument to mathematical function" w
... Dear Stafano, I think the ID from the non model organism may cause the error. Would you please tell me the specie you tested and send me some of your genes. So that I can have a try. Thank you! Best, Shilin 2014-09-13 3:03 GMT-05:00 stefano romano : > Hi, > > I am using KEGGprofile to p ...
written 3.7 years ago by zhao shilin60
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Answer: A: Fwd: Paired Data Analysis in baySeq package
... Thanks Tom. I think I misunderstood the experiment design here for pair data. As you said, the experiment design was : Samples Patients Tissue Response 1 1 Normal Y 2 2 Normal Y 3 3 Normal N 4 4 Normal N 5 1 Tumor Y 6 2 Tumor Y 7 3 Tumor N 8 4 Tumor N Now I can unders ...
written 4.3 years ago by zhao shilin60
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Paired Data Analysis in baySeq package
... Hi all, Is there anybody who is familiar with the Paired Data Analysis in baySeq package. I'm following the instructions in its vignette. I used: library(baySeq) data(pairData) pairCD <- new("pairedData", data = pairData[,1:4], pairData = pairData[,5:8],replicates = c(1,1,2,2),groups = list(NDE ...
bayseq written 4.3 years ago by zhao shilin60
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Comment: C: error installing KEGGSOAP
... Hi all, I think what Martin said is exact. The primary function of KEGGprofile package is plot_pathway, which uses the latest files in the KEGG website. So the final result figure which represents the gene expression in each pathway is up-to-date. Because find_enriched_pathway needs a list with gen ...
written 5.3 years ago by zhao shilin60
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Comment: C: Kegg Profile package problem
... Hi Dan, I'm very happy to know that some other persons were using my package. And it is the first time that some persons ask me questions about it in the mail list. For your question, the web page "http://www.genome.jp/kegg/pathway/map/map00910.html" indicated that: The biological process of the n ...
written 5.4 years ago by zhao shilin60

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