User: Nianhua Li

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Nianhua Li870
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13 years, 6 months ago
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Posts by Nianhua Li

<prev • 87 results • page 2 of 9 • next >
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Answer: A: Annotation of U95av2 array
... Hi, James and George, The source data that we used for building the current hgu95av2 package in bioc 2.0 was downloaded on Feb 28, 2007. Hs.443948 was linked with 3576 in the source data. Unfortunately, it is too late to update the packages at this time. The way it works is that we download all th ...
written 12.3 years ago by Nianhua Li870
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Answer: A: homology package question
... Hi, James, The source file of mmuhomology is ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/hmlg.ftp (download on 02/28/2007) and the description is ftp://ftp.ncbi.nih.gov/pub/HomoloGene/README-old According to the description, the 4th and 7th column of hmlg.ftp are Entrez Gene ID, the 5th and 8th ...
written 12.3 years ago by Nianhua Li870
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Answer: A: hyperGTest, KEGG
... Hi, Ivan, library(KEGG, lib="~/annoprep/bin-13") x <- c("04360", "05214", "01030") ## Assume Hu19K8Build17102006 is the annotation for human genes, ## you prefix the KEGG ID with human KEGG pathway code "hsa" x <- paste("hsa", x, sep="") g <- mget(x, KEGGPATHID2EXTID) ## then maybe you wan ...
written 12.4 years ago by Nianhua Li870
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Answer: A: I need more precision about annotation of HGU133plus
... Hi, Gregory, The package hgu133plus2 is maintained by our team at the Department of computational biology at Fred Hutchinson Cancer Research Center at Seattle, WA. We are part of the biocore team (i.e. the core team of bioconductor). The package is updated once every six months by using another R p ...
written 12.4 years ago by Nianhua Li870
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Answer: A: Problems in AnnBuilder package function ABPkgBuilder
... Hi, Asta, > So my package is built 7 days after the official packet. Even though the package was "published" on Marth 15, the source data was downloaded from public data resources on Feb 28. So the differences in source data are about 3 weeks. > I use the public representative id from rat23 ...
written 12.4 years ago by Nianhua Li870
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Failed to obtain KEGG organism code
... Dear Tae-Hoon, Thanks for the bug report. KEGG changed their FTP site structure on March 31. I have updated AnnBuilder. The lastest version is 1.13.23 which is available at svn repository now. You can get it via biocLite tomorrow. thanks nianhua ...
annbuilder written 12.4 years ago by Nianhua Li870
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Answer: A: AnnBuilder GO url question
... Hi, Tae-Hoon, Even if accessing GO website is a problem, it won't affect your custom annotation package. There are only 3 objects in the custom package that are related to GO: GO, GO2PROBE and GO2ALLPROBES. Here I use to represent your package name. GO and GO2PROBE are created by using direct mapp ...
written 12.4 years ago by Nianhua Li870
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Answer: A: problem when using "humanCHRLOC"
... Hi, Isn't it a solved issue?! http://thread.gmane.org/gmane.science.biology.informatics.conductor/11 908/focus=11926 The latest version is 1.15.12. nianhua ...
written 12.4 years ago by Nianhua Li870
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Answer: A: Pathways missing
... Hi, Mayte, The hgu133a2 you are using is the most updated version in bioconductor, but the source data that we used to build this package was download in Aug, 2006. There will be more updated data packages (source and windows binaries) available before next Thursday (actually maybe this Thursday). ...
written 12.5 years ago by Nianhua Li870
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Comment: C: ABPkgBuilder trouble
... Hi, Johan, A couple of questions/suggestions and one offer: 1. You mentioned that you have tried AnnBuilder on two windows computers. Could you try just the perl script I sent to you in my last email and tell me the result? 2. Did you see the perl warning about locale warning when you ran the per ...
written 12.5 years ago by Nianhua Li870

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