User: Arman Shahrisa

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Posts by Arman Shahrisa

<prev • 16 results • page 1 of 2 • next >
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Is there any prerequisites for taking correlation in genomic data?
... I know this question might not be related to Bioconductor but I couldn't think of anywhere else. When I take correlation between two genes, should I exclude genes that their expression is not meaningful? Additionally, should I exclude samples that their z-score is under e.g. z-score = 2? Or should I ...
correlation written 3 months ago by Arman Shahrisa10 • updated 3 months ago by chris86380
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Comment: C: How can I find the location of a gene based on cytogenetic bands (e.g. 7q31.2)?
... Exactly! Thank you very much. ...
written 8 months ago by Arman Shahrisa10
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How can I find the location of a gene based on cytogenetic bands (e.g. 7q31.2)?
... How can I find the location of a gene based on cytogenetic bands (e.g. 7q31.2)? Is there any package(s) that lets me convert the gene symbol to cytogenetic bands? ...
bioconductor cytogenetics written 8 months ago by Arman Shahrisa10 • updated 8 months ago by Martin Morgan ♦♦ 21k
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How can I mention separate creator and correspondence in a package?
... I'm developing a Bioconductor package in which I'm a creator, author, and maintainer. But someone else is the corresponding author. Is the following code correct in the package description?   Author: c(person(first = "A****", last = "S*******",                             email = "s*************** ...
package description written 13 months ago by Arman Shahrisa10 • updated 13 months ago by Martin Morgan ♦♦ 21k
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Comment: C: I'm developing a package. How can I specify a dependent package to be installed
... Hi, My package requires "xlsx" package to export data as excel files. Even with java runtime environment installed, R returns an error during the installation of "xlsx" package. I googled it and found "install.packages("xlsxjars", INSTALL_opts = "--no-multiarch")" in a forum. It fixed the problem f ...
written 13 months ago by Arman Shahrisa10
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I'm developing a package. How can I specify a dependent package to be installed with an option?
... I'm developing a package. How can I specify a dependent package to be installed with an option? For example, inside description file: Depends: cgdsr, xlsx, gplots, RColorBrewer, rafalib, Biobase, genefilter, xlsxjars I manually install the "xlsxjars" package as "install.packages("xlsxjars", INSTA ...
package dependency written 13 months ago by Arman Shahrisa10 • updated 13 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: How to create automated cbind in a for loop
... I fixed the problem. It was a "E" instead of "e". I appreciate for your time. ...
written 2.4 years ago by Arman Shahrisa10
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How to create automated cbind in a for loop
... How can I create an automated cbind() to use with for loop? This is the part that returns error expression <- cbind(expression, rrM.ProfileData) The following is my function genes is a character vector containing names of the desired genes. cancer is also a character vector string containin ...
loop matix written 2.4 years ago by Arman Shahrisa10 • updated 2.4 years ago by Martin Morgan ♦♦ 21k
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Comment: C: Database download ends with error for AnnotationHub
... The command "hubCache(hub)" returns the following error: Error in hubCache(hub) : error in evaluating the argument 'x' in selecting a method for function 'hubCache': Error: object 'hub' not found also > traceback() 1: hubCache(hub) So I wasn't able to remove the files by command. Instead, ...
written 3.1 years ago by Arman Shahrisa10
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Answer: A: Database download ends with error for AnnotationHub
... I don't have stable HTTPS connection. I performed your commands but every time it finishes with the same error. Is there anyway to manually download databases and put them in corresponding folder? By the way, I'm using R 3.1.3 and I can't upgrade it due to limitations of class to strictly use R 3.1 ...
written 3.1 years ago by Arman Shahrisa10

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Popular Question 13 months ago, created a question with more than 1,000 views. For Database download ends with error for AnnotationHub

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