User: niutster

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niutster0
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Posts by niutster

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reading text file in R
... Hi, I have 6 text files contain chromosome's  name, start, and end and probe's name and CpG numbers. I want to read these files in R and then do some processes with this data. Used commands are in below: my_data <- read.delim("Chr.txt",header=TRUE, sep="\t") d=as.numeric(my_data[1,1]) > my_ ...
text warning read.delim written 29 days ago by niutster0 • updated 28 days ago by Gordon Smyth31k
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Minfi reading command error
... Hi, I am using minfi version 1.23 but when i want to use  read.metharray.exp() command get this error: Error in xx$Quants[commonAddresses, "Mean"] : subscript out of bounds  while using older version of minfi which uses read.450k.exp() i dont get this. library(minfi) require(minfi) baseDir< ...
cdf minfi error read.metharray.exp command written 10 weeks ago by niutster0
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Finding DOSE package for R3.3.3
... Hi, I searched for a version of DOSE >= 2.11.12 in windows that is compatible to R3.3.3 but in bioconductor (https://bioconductor.org/packages/release/bioc/html/DOSE.html) there was not any DOSE updated version for windows.     ...
R package installation written 4 months ago by niutster0 • updated 4 months ago by Hervé Pagès ♦♦ 12k
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Error in installing ReactomePA
... Hi, I want to do pathway analysis with "ReactomePA" in R, I installed all dependencies but I get this error: Error : Functions found when exporting methods from the namespace ‘S4Vectors’ which are not S4 generic: ‘grep’, ‘grepl’ Error: package or namespace load failed for ‘DOSE’   ...
R package written 4 months ago by niutster0 • updated 4 months ago by Martin Morgan ♦♦ 20k
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seqlm installation error
... Hi, I faced an error while installing "seqlm" package in R 3.2.1 in windows OS, by these commands: library(devtools) install_github("raivokolde/seqlm") , error: Error in curl::curl_fetch_disk(url, x$path, handle = handle) : SSL peer certificate or SSH remote key was not OK How can i fix it? Thank ...
software error R installation written 6 months ago by niutster0 • updated 6 months ago by Marcel Ramos ♦♦ 50
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removing probes representing in a certain beads
... Hi, I want to remove probes not representing by a certain numbers of beads on array in minfi tool, anybody know how can do it? Thanks ...
preprocessing probe minfi written 6 months ago by niutster0
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effective tools, methylation data
... Hi, I want to analysis methylation data, but i dont  know which tools is better, for example : minfi, CHAMP, seqlm,... Thanks ...
bioconductor illimina 450k methylation written 6 months ago by niutster0 • updated 6 months ago by James W. MacDonald44k
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Comment: C: minfi probe removal
... Thanks for your answer. ...
written 6 months ago by niutster0
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Comment: C: minfi probe removal
... Thanks, but minfi's objects are RGset or Methylset. There are not any eset. ...
written 6 months ago by niutster0
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minfi probe removal
... Hi, I am using minfi to pre-processes methylation files but i don't know how can I remove probes with a certain p-value, there is not any command in tutorial to tell me about it. Thanks   ...
probe minfi written 6 months ago by niutster0 • updated 6 months ago by James W. MacDonald44k

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