User: Asma rabe

gravatar for Asma rabe
Asma rabe290
Reputation:
290
Status:
Trusted
Location:
Japan
Last seen:
1 year, 4 months ago
Joined:
8 years ago
Email:
a********@gmail.com

Posts by Asma rabe

<prev • 99 results • page 2 of 10 • next >
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Error when installing ReportingTools
... Hi, I got this error while installing ReportingTools: Error in download.file(url, destfile, method, mode = "wb", ...) :   cannot download all files In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) :   URL 'https://bioconductor.org/packages/3.4/bioc/src/contri ...
reportingtools written 2.9 years ago by Asma rabe290
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Comment: C: UCSC web service API
... I have downloaded another packages and restarted R session. Using session Info(), I found that old rtracklayer package is running rtracklayer_1.30.4 instead of rtracklayer 1.33.9 How to uninstall rtracklayer_1.30.4 ?? ...
written 2.9 years ago by Asma rabe290
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Comment: C: minfi devel error
... Thanks Martin. It works. I installed minfi/bump hunter in a separate R session. In addition, I restarted the old R session to load the library. I do not fully understand the database of available packages in my R session is stale? ...
written 2.9 years ago by Asma rabe290
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Positions to genes in minfi
... Hi, I used minfi package to analyze 450K methylation data. I got a list of regions that are differentially methylated. I would like to know how can i convert the DMR regions into genes to asses which genes are hypo/hyper methylated. Thank you. ...
genomicranges minfi written 2.9 years ago by Asma rabe290
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minfi devel error
... Hi, I am trying to download devel version of minfi , I got an error due to dependency error of bump hunter library Any idea? ################ biocLite("minfi") BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.23.5), R 3.3.0 (2016-05-03). Installing package(s) 'minfi ...
bumphunter written 2.9 years ago by Asma rabe290 • updated 2.9 years ago by Martin Morgan ♦♦ 23k
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Comment: C: UCSC web service API
... Thank you ! ...
written 3.0 years ago by Asma rabe290
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Comment: C: UCSC web service API
... Thank you Martin and Tom for kind help. It seems the problem was related to rtracklayer version. devel version works well  I can access  http://genome-asia.ucsc.edu using web browser. However, I got an error when I tried  options(Gviz.ucscUrl="http://genome-asia.ucsc.edu") session <- browser ...
written 3.0 years ago by Asma rabe290
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Comment: C: UCSC web service API
...   Thank you. I installed devel version from http://bioconductor.org/packages/devel/bioc/html/rtracklayer.html source("https://bioconductor.org/biocLite.R") biocLite("rtracklayer") but i still have the same error!! ...
written 3.0 years ago by Asma rabe290
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UCSC web service API
... Hi, when i try to set the genome to hg19, I got the following error: genome(session) <- "hg19" Error in `genome<-`(`*tmp*`, value = "hg19") : Failed to set session genome to 'hg19' # I set the proxy on my machine before i run R. Thank you in advance   ...
rtracklayer txdb.hsapiens.ucsc.hg19.knowngene written 3.0 years ago by Asma rabe290 • updated 3.0 years ago by Martin Morgan ♦♦ 23k
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Comment: C: Error when using Gviz
... Thanks Folrian ! Yeah, it fails with hg19 but not with hg38. Any suggestions? genome(session) <- "hg38" #works fine genome(session) <- "hg19" Error in `genome<-`(`*tmp*`, value = "hg19") :    Failed to set session genome to 'hg19' ...
written 3.0 years ago by Asma rabe290

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Popular Question 16 months ago, created a question with more than 1,000 views. For RPKM and FPKM
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Scholar 3.3 years ago, created an answer that has been accepted. For A: minfi starting from beta values

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