User: yanju@liacs.nl

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Posts by yanju@liacs.nl

<prev • 16 results • page 1 of 2 • next >
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Comment: C: chromosome plot
... Hello Seth, I was trying to use writeChrLength in AnnBuilder package like follows: > library("annotate") > library("geneplotter") > library("AnnBuilder") > library(zebrafish) > path <- file.path(.path.package("zebrafish")) > writeChrLength("zebrafish","/usr/local/lib/R/s ...
written 12.5 years ago by yanju@liacs.nl160
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chromosome plot
... Dear all, I was trying to visualize genes in each chromosomes in Zebrafish. I found how people visualize them in Human species using geneplotter. Then I tried followings: > library("annotate") > library("geneplotter") > library(zebrafish) > newChrom<-buildChromLocation("zebrafis ...
zebrafish geneplotter written 12.5 years ago by yanju@liacs.nl160 • updated 12.5 years ago by Seth Falcon7.4k
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how to do quantile normalization under dye swape situation
... Hello All, my microarray datasets are like follows. And I want to normalize the data. Targets: Sample FileName Dye Stage Cy3 Cy5 ZWS57 57.gpr T5C3 high oblong ref high ZWS58 58.gpr T3C5 high oblong high ref ZWS61 61.gpr T5C3 high oblong re ...
microarray written 12.6 years ago by yanju@liacs.nl160 • updated 12.6 years ago by J.delasHeras@ed.ac.uk1.9k
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about ts.plot
... Dear all, I was tring to plot Multiple Time Series using ts.plot. Then I want to give each time series a color. My code is like follows: color<-rainbow(ncol(ts)) ts.plot(ts,col=color) then I got colorful lines, but I dont know which line is corresponding to which color. How to settel this prob ...
written 12.8 years ago by yanju@liacs.nl160 • updated 12.8 years ago by James W. MacDonald52k
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about gene annotation
... Hello all, I was tring to annotate zelbrafish microarray data using genbank function, but I got the following errors. Could you tell me what the problem is? library(XML) library(annotate) genbank("AW116961") Entity: line 47: parser error : Opening and ending tag mismatch: link line 2 ...
microarray annotate written 12.9 years ago by yanju@liacs.nl160 • updated 12.9 years ago by James W. MacDonald52k
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grid package
... Dear ALL, When i was trying to install "Hexbin" package in R, I have got the follows error message: Loading required package: grid Error: package 'grid' could not be loaded But I couldnt find grid package anywhere. My R is 2.3 verson and I am using debian system. Anyone give me any sugguestions? ...
written 13.0 years ago by yanju@liacs.nl160 • updated 13.0 years ago by Hervé Pagès ♦♦ 14k
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Comment: C: Normalization between arrays for common reference, time course and direct two co
... Hello Jenny and all, I tried to used "duplicateCorrelation" , then fit MAlist to the linear model by using the correlation. Theoritically, FIT will contain half as many row as MA (2 replicates within one array). But in my case, the gene number in FIT, doest not change. I still got replicates within ...
written 13.0 years ago by yanju@liacs.nl160
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background correction
... Dear all, As read from the instruction of backgroundCorrect in limma, the method "half", "minimum", "edwards" and so on are all designed to produce positive corrected intensities. My code is as follows: rgc<-backgroundCorrect(rg, method="half") plotDensities(rgc) After I plot the gr ...
graph limma written 13.0 years ago by yanju@liacs.nl160 • updated 13.0 years ago by Jenny Drnevich2.2k
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about: p.value, adj.p.val, F.p.value
... Dear all, I am just a little bit confused about p.value, adj.p.value and F.p.value. Could somebody tell me what are the proper cases to use them? I am supposed to detect the differenct expressed genes with the p-value less than 0.05, therefore, my code is like follows: fit<-eBayes(fit) s ...
limma written 13.0 years ago by yanju@liacs.nl160 • updated 13.0 years ago by Weiwei Shi1.2k
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Comment: C: problems about cDNA vs genomic arrays normalization
... Hello Jenny, I also realized the first problem you mentioned after I sent the email to you. After I change it, the results seems better, not very much markers appeared in the list. Thank you very much for your suggestion during these two days. I think for the time being, my questions have been sett ...
written 13.1 years ago by yanju@liacs.nl160

Latest awards to yanju@liacs.nl

Popular Question 12.5 years ago, created a question with more than 1,000 views. For grid package
Popular Question 12.5 years ago, created a question with more than 1,000 views. For about: p.value, adj.p.val, F.p.value
Popular Question 12.5 years ago, created a question with more than 1,000 views. For about: p.value, adj.p.val, F.p.value

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