User: Yoo, Seungyeul

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Posts by Yoo, Seungyeul

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Encrypting IDAT files using IDATreader
... Dear Mike, Thank you so much for your detail explanation. That helped me a lot to understand the result from IDATreader. Also thanks for your work to build this package. =) Best regards, Seungyeul Yoo Postdoctoral Fellow Jun Zhu's Laboratory Institute of Genomics and Multiscale Biology Departm ...
written 7.0 years ago by Yoo, Seungyeul110
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Comment: C: Encrypting IDAT files using IDATreader
... Dear Mark, Thanks for sharing "lumidat" package with me. I think it works fine now. But I'm wondering if an argument "convertNuID" is available in lumiR.idat(). When I ran it it failed with error like following. > res<-lumiR.idat(filenames,manifestfile="HumanHT- 12_V4_0_R1_15002873_B.txt",na ...
written 7.0 years ago by Yoo, Seungyeul110
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Comment: C: Encrypting IDAT files using IDATreader
... Hi Mike, Thank you so much for your advice. I can now install it properly and succeeded to read a idat file. After I read a idat file, then it contains information something like following. > idat[1:10,] MeanBinData TrimmedMeanBinData DevBinData MedianBinData BackgroundBinData BackgroundDev ...
written 7.0 years ago by Yoo, Seungyeul110
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Encrypting IDAT files using IDATreader
... Hi all, I'm trying to analyze Illumina array of gene expression. The file format is .idat which is encrypted data. I downloaded IDATreader packages as Mike suggested in some of previous post. I also install openssl for my mac os x. http://www.compbio.group.cam.ac.uk/software/idatreader But when I ...
genetics written 7.0 years ago by Yoo, Seungyeul110 • updated 7.0 years ago by Mike Smith3.9k
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How can I identify the closest transcript from a chromosome coordinate?
... Dear all, I'm working on a DNA Methylation microarray dataset. The microarray design is "pd.feinberg.hg18.me.hx1". I used the CHARM package to estimate methylation percentile and selected 1000 probes having larger variances of methylation level across samples. The 1000 probe are identified as chr ...
microarray genetics probe charm written 7.1 years ago by Yoo, Seungyeul110
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Comment: C: How can I obtain gene name from chromosome location?
... Hi Tim, Thank you for your advices. I'm sorry for another naive questions, but how can I know whether the chromosome location are promoter regions or not from the rawdata? I'm reading rawdata of DNA methylation which is a pair of untreated and methylated .xys files like followings. pd<-read.ta ...
written 7.1 years ago by Yoo, Seungyeul110
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Comment: C: How can I obtain gene name from chromosome location?
... Hi Steve, I really appreciate your comments. The pipeline was what I want to know. I will try to follow the steps and post another questions if I'm stuck somewhere else. I'm a newbie in the genomics but really enjoy learning all these stuffs. Thanks again. Seungyeul Yoo Postdoctoral Fellow Depa ...
written 7.1 years ago by Yoo, Seungyeul110
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How can I obtain gene name from chromosome location?
... Hi all, I'm working on DNA-methylation data of Lung Genomes. I'm using CHARM packages for the analysis of differentially methylated regions. I can have a list of chromosomal locations indicating genes but I don't know how I map this location into specific gene names. > head(pns) [1] "chr19:42 ...
lung charm genomes written 7.1 years ago by Yoo, Seungyeul110 • updated 7.1 years ago by Steve Lianoglou12k
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Merging two tilingfeaturesets into one set.
... Hello, I'm working on dna methylation microarray. I need to merge two sets into one set. > rawData $v1 TilingFeatureSet (storageMode: lockedEnvironment) assayData: 2197815 features, 59 samples element names: channel1, channel2 protocolData rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010 ...
microarray genetics annotation written 7.2 years ago by Yoo, Seungyeul110
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Scaling color range of heatmap.2 with scaled row option
... Hi, I am trying to draw a heatmap of microarray datasets. I'm using a heatmap.2 function of gplots as following: heatmap.2(var_exp,col=greenred,trace="none",scale="row",symkey=TRUE,hc lust=function(x) hclust(x,method="complete"),distfun=function(x) as.dist(1-cor(t(x)))) It generates a fine heatm ...
microarray genetics clustering written 7.2 years ago by Yoo, Seungyeul110

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