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 7 months ago by Arman Shahrisa10 • updated 7 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 12 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 12 months ago by Arman Shahrisa10 • updated 12 months ago by Martin Morgan ♦♦ 22k
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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 16 months ago by Arman Shahrisa10 • updated 16 months ago by Martin Morgan ♦♦ 22k
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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 16 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 16 months ago by Arman Shahrisa10 • updated 16 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 2.7 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 2.7 years ago by Arman Shahrisa10 • updated 2.7 years ago by Martin Morgan ♦♦ 22k
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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 3.4 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 3.4 years ago by Arman Shahrisa10

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Popular Question 16 months ago, created a question with more than 1,000 views. For Database download ends with error for AnnotationHub

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