User: Jianping Jin

gravatar for Jianping Jin
Jianping Jin890
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8 years, 10 months ago
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14 years, 6 months ago
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j***@email.unc.edu

Posts by Jianping Jin

<prev • 88 results • page 1 of 9 • next >
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Answer: A: booklet on using R for biomedical statistics
... Hi Avril, A great work. Wondering is there any chapter for survive study? JP- -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Coghlan, Avril Sent: Monday, December 13, 2010 9:38 AM To: bioconductor at r-project.org Subj ...
written 8.9 years ago by Jianping Jin890
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Comment: C: need help on
... Dear Marco, Thank you very much for your quick reply! What I was trying to do was to extract the comparisons of age group 1 and group 2 in male, or group 3 vs group 4 in female, or between groups of male and female. Please see the following chart: Contrasts Levels M.8vs10 F.12vs1 ...
written 9.0 years ago by Jianping Jin890
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need help on
... Dear statisticians of the list, I am a limma user and have a small data set that I used the lme mixed effect model for analysis. I need some help in extracting comparisons from the result. I sent my questions to the R help list, but it appears that there is no people there care about the questions. ...
limma written 9.0 years ago by Jianping Jin890 • updated 9.0 years ago by Manca Marco PATH340
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64-bit R
... Dear list, I would want to install R/bioconductor to my 64-bit machine with Windows 7 installed. When are the 64-bit R build and bioconductor available? will R 2.11 are Bio C 2.6 work with Windows 7? Thanks, Jp Jin [[alternative HTML version deleted]] ...
written 9.6 years ago by Jianping Jin890 • updated 9.6 years ago by Martin Morgan ♦♦ 23k
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Ringo question
... Dear Joern, In the PLos paper, to find ChIP-enriched regions MAs data were "rbind" (MA <- do.call("rbind", MAs), and then find ChIP enriched regions based on smoothX using "findChersOnSmoothed". I am wondering if this function takes sample replicates into calculation. If not, how can I get the ...
written 10.7 years ago by Jianping Jin890
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Comment: C: chipAlongChrom problem in Ringo
... Hi Joern, I used the code on the PLos article to summarize the GO terms with the ChIP-enriched regions. But I got some problems in sigGOTable: NFRes <- sigGOTable(NFOnlygenes) . . Level 2: 18 nodes to be scored (17 eliminated genes) Level 1: 1 nodes to be scored ...
written 10.7 years ago by Jianping Jin890
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Comment: C: chipAlongChrom problem in Ringo
... Hi Joern, You are right. I need to generate y0 for the plot. Here is another trouble: > plot(chersX[[which.max(chersXD$maxLevel)]],smoothX,probeAnno=probeAn no, gff=mm9genes2, paletteName="Dark2", ylim=c(-1,6)) Error in as.double(x) : cannot coerce type 'S4' to vector of type 'double' chipA ...
written 10.7 years ago by Jianping Jin890
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Comment: C: chipAlongChrom problem in Ringo
... Thanks for your quick reply. > table(probeAnno["5.index"] %in% featureNames(X)) FALSE 21152 What are feature names in probeAnno? Actually I used a new output file from the script you edited to generate probeAnno with no complain: probeAnno <- posToProbeAnno("C:/from_DriveD/Chip- chip/Bultm ...
written 10.8 years ago by Jianping Jin890
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chipAlongChrom problem in Ringo
... Hi list, I ran into a problem using chipAlongChrom to visualize a Chip chip array intensities: > chipAlongChrom(X,chrom="5", probeAnno=probeAnno,gff=mm9genes2, xlim=c(37.63e6, 37.64e6), ylim=c(-3,5), paletteName="S et2") Getting probe intensities in selected regions.., Preparing color scheme... ...
probe written 10.8 years ago by Jianping Jin890 • updated 10.7 years ago by Joern Toedling720
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Comment: C: RinGO problem
... Hi Joern, There are 6247 probes with LENGTH <= 0 (actually <= -50). The minus sign may refer to the genome strain. I checked the demo data set which also contains minus values for LENGTH. The only difference I can tell is the format of PROBE_ID. In the demo file it is something beginning wit ...
written 10.8 years ago by Jianping Jin890

Latest awards to Jianping Jin

Great Question 8.9 years ago, created a question with more than 5,000 views. For how to check BioConductor version?
Popular Question 8.9 years ago, created a question with more than 1,000 views. For how to check BioConductor version?
Popular Question 8.9 years ago, created a question with more than 1,000 views. For how to check BioConductor version?

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