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Questions tagged [bioconductor]

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.

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R on MacOS Error: vector memory exhausted (limit reached?)

I'm trying to run an R script (in particular, I am using the "getLineages" function from the Bioconductor package, Slingshot. I'm wondering why the error "vector memory exhausted (limit reached?)" is showing up when I use this function, as it…
Anjan Bharadwaj
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installation path not writable R, unable to update packages

I am trying to install Bioconductor into R, using the code on their website. When I type in the code (see bellow) I get an error message saying that some packages can't be updated, the installation path is unwriteable. > ## try http:// if https://…
Eleanor Bellows
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differences in heatmap/clustering defaults in R (heatplot versus heatmap.2)?

I'm comparing two ways of creating heatmaps with dendrograms in R, one with made4's heatplot and one with gplots of heatmap.2. The appropriate results depend on the analysis but I'm trying to understand why the defaults are so different, and how to…
user248237
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2 answers

How can I convert Ensembl ID to gene symbol in R?

I have a data.frame containing Ensembl IDs in one column; I would like to find corresponding gene symbols for the values of that column and add them to a new column in my data frame. I used bioMaRt but It couldn't find any of the Ensembl IDs! Here…
user3576287
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Plotting confidence intervals with NA values

I would like to plot confidence intervals to a data with NAs, using Gviz package. I modified manual example to expose my problem. First as the manual expose: library(Gviz) ## Loading GRanges object data(twoGroups) ## Plot data without NAs dTrack…
user2120870
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package cannot be unloaded in R: cannot install package

I am trying to install a package in R, but cannot get around the following error. What is going on? :( I am running Fedora 20, R 3.2 biocLite("monocle") BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller…
gaelgarcia
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in R how to get error messages in english

I am trying some tutorials on bioconductor; but I get error messages, that I would like to search/submit; unfortunately, since R is installed on a system configured in french, R returns me messages in french; how could I have these messages in…
user1706600
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CRAN Package Depends on Bioconductor Package Installing error

I manage the Depends, suggests and imports of the description file. and finally I submit my package to CRAN. But during installation the package, it only install the packages which are deposited under CRAN not for bioconductor packages. besides, it…
Mikael
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“Non Zero Exit Status” R 3.6.0 "Biobase"

I need to install different packages on R. The OS is ubuntu for windows. When I try "BiocManager::install("Biobase") I get the following error: ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help…
Mark Wekking
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3 answers

Map SNP IDs to genome coordinates

I have several SNP IDs (i.e., rs16828074, rs17232800, etc...), I want to their coordinates in a Hg19 genome from UCSC genome website. I would prefer using R to accomplish this goal. How to do that?
user1938809
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Subset by samples for an ExpressionSet object

I have an ExpressionSet object with 100 samples: > length(sampleNames(eset1)) 100 I also have a vector of the names of 75 samples (not the data itself): > length(vecOf75) 75 How can I subset eset1 (and save it) according to the 75 sample names?…
user1202664
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R + Bioconductor : combining probesets in an ExpressionSet

First off, this may be the wrong Forum for this question, as it's pretty darn R+Bioconductor specific. Here's what I have: library('GEOquery') GDS = getGEO('GDS785') cd4T = GDS2eSet(GDS) cd4T <- cd4T[!fData(cd4T)$symbol == "",] Now cd4T is an…
Mike Dewar
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All NaNs in RMA normalization of GSE31312 using Brainarray custom CDFs

I'm trying to RMA normalize a particular gene expression dataset concerning diffuse large B-cell lymphoma using custom gene-level annotation CDF (chip definition file) files from Brainarray. Unfortunately, the RMA normalized expression matrix is all…
Anders Ellern Bilgrau
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How to plot overlapping ranges with ggplot2

I am trying to get my head around ggplot2. In particular, I am trying to find out if there is a better (more elegant, simpler) way of creating the plot found in the Bioconductor IRanges package vignette (found here, figure on page 12, code on page…
Andreas
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How to perform clustering without removing rows where NA is present in R

I have a data which contain some NA value in their elements. What I want to do is to perform clustering without removing rows where the NA is present. I understand that gower distance measure in daisy allow such situation. But why my code below…
neversaint
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