User: Nianhua Li

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Nianhua Li870
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Posts by Nianhua Li

<prev • 87 results • page 1 of 9 • next >
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Answer: A: Annotations dealing with "removed" refseq record
... Hi, Francois, If I remember correctly, we had a hard time finding up-to-date annotations from Agilent. The annotation file we downloaded from Agilent was out-of- date. We still update the annotation packages for each release, but probeset to gene mapping (recorded in mgug4122aACCNUM) hasn't been up ...
written 12.1 years ago by Nianhua Li870
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Answer: A: Re : bug with AnnBuilder and parser
... Hi Gregory, I couldn't repeat your error with your base mapping file. I am using linux though. The script I used was: library(AnnBuilder) ABPkgBuilder(baseName="probeset_gb.txt", baseMapType="gbNRef", pkgName="monPackageAnnoted", pkgPath=". ...
written 12.2 years ago by Nianhua Li870
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Comment: C: Building the tomato annotation library(Affy)
... Dear Dr. Philip de, > > which is a minimal improvement compared what was obtained first. Using unigene (instead of gb) did not improve it (on the contrary). The only problem I have now is that the GO-annotation is totally missing, whereas it is available in the Affymetrix annotation library. ...
written 12.2 years ago by Nianhua Li870
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Answer: A: Building the tomato annotation library(Affy)
... Dear Dr Philip de Groot, Thanks for the report and sorry for the late reply. The "refLink.txt" error was intended, but we have changed it to a more informative message. The "sort.list" error was a bug. It happens when parsing KEGG pathway/enzyme data. The KEGG data file usually contains both pathw ...
written 12.2 years ago by Nianhua Li870
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Answer: A: bug with AnnBuilder and parser
... Hi, Gregory, Could you try invoking ABPkgBuilder directly? Here is a sample script (taken from your email) for example: library (AnnBuilder) data_gb = read.table("probeset_gb.txt" , sep = "\t", header=FALSE, as.is=TRUE) mybase = file.path("probeset_gb.txt") mybasetype= "gb" mydir = getwd() ABPkgB ...
written 12.2 years ago by Nianhua Li870
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Re : bug with AnnBuilder and parser
... Hi, gregory, I also cc the list since it will benefit others. You'd better update your R and AnnBuilder. R 2.5 has just released last month. After installing R, please use "biocLite()" to get the latest AnnBuilder (1.14.0 for R 2.5 and 1.15.2 for R 2.6) and try from there. Your file permissions for ...
annotate annbuilder written 12.2 years ago by Nianhua Li870
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Answer: A: AnnBuilder with custmerized GO annotation
... Hi, Xinxia, I believe the problem is related to the data. The data is was created a couple of years ago. I guess maybe we updated the parser according to the changes on GO website, but didn't update the data. The data is mean to be an example and definitely won't be consistent with latest GO data. ...
written 12.2 years ago by Nianhua Li870
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Answer: A: about source to make HGU133plus2 package
... Hi, Greg, We first map probeset IDs to Entrez Gene IDs and then extract other annotations by using the Entrez Gene IDs. Here are some details for hgu133plus2 v1.16.0 (the one in bioc2.0 release). The ACCNUM environment (hgu133plus2ACCNUM) was extracted from Affymetrix's annotation file (dated 11/1 ...
written 12.2 years ago by Nianhua Li870
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Answer: A: Editing AnnBuilder function "getSrcUrl"
... Hi, Dermot, I have updated AnnBuilder to support cattle. Please use "Bos taurus" as organism name when you invoke ABPkgBuilder. Here is an example script: library(AnnBuilder) ABPkgBuilder(baseName="bovine.GenBankID", baseMapType="gbNRef", pkgName="bovine", ...
written 12.2 years ago by Nianhua Li870
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Answer: A: Editing AnnBuilder function "getSrcUrl"
... Hi, Dermot, Bos Taurus is a fairly popular organism. I will try to make AnnBuilder support Bos Taurus. It might take a couple of days. But I have to commit the modification to bioc 2.1 because BioC 2.0 has just been released. best nianhua ...
written 12.2 years ago by Nianhua Li870

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