bioconductor

“Non Zero Exit Status” R 3.6.0 “Biobase”

由 眉间皱痕 提交于 2019-12-01 19:34:16
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 indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries mv: cannot move '/home/mark/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Biobase/00new/Biobase' to '/home/mark/R/x86_64-pc-linux-gnu-library/3.6/Biobase':

in R how to get error messages in english

由 喜你入骨 提交于 2019-12-01 14:05:54
问题 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 english. My system: Ubuntu 10.04 runing gnome 3; R version is the last (2.15.1) Bioconductor have been updated to 2.10, and I try to download/use datasets GSE20986 (but I have had a similar error with another dataset GSE2034, while following the

R Bioconductor installation error - Line starting '< DOCTYPE html PUBLI …' is malformed

由 本秂侑毒 提交于 2019-12-01 13:30:22
I'm having trouble installing bioconductor packages in R. This is on MacOSX, a fresh install of R 2.15, and using bioconductor 1.4.4. Transcript follows: > source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.4.4, ?biocLite for help > biocLite("Biobase") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.4. Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15 Installing package(s) 'Biobase' Error: Line starting '<!DOCTYPE html PUBLI ...' is malformed! > traceback() 6: read.dcf

How to perform clustering without removing rows where NA is present in R

由 不问归期 提交于 2019-11-30 04:14:22
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 doesn't work? I welcome other alternatives than 'daisy'. # plot heat map with dendogram together. library("gplots") library("cluster") # Arbitrarily assigning NA to some elements mtcars[2,2] <- "NA" mtcars[6,7] <- "NA" mydata <- mtcars hclustfunc <- function(x) hclust(x, method="complete") # Initially I wanted to use this but it didn't take NA #distfunc

BioMart: Is there a way to easily change the species for all of my code?

由 落爺英雄遲暮 提交于 2019-11-29 16:56:56
Below is a small fraction of my code: library(biomaRt) ensembl_hsapiens <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") hsapien_PC_genes <- getBM(attributes = c("ensembl_gene_id", "external_gene_name"), filters = "biotype", values = "protein_coding", mart = ensembl_hsapiens) paralogues[["hsapiens"]] <- getBM(attributes = c("external_gene_name", "hsapiens_paralog_associated_gene_name"), filters = "ensembl_gene_id", values = c(ensembl_gene_ID) , mart = ensembl_hsapiens) This bit of code will only allow me to extract the paralogues for hsapiens, it there a way for me to easily get the

installation path not writable R, unable to update packages

由 半腔热情 提交于 2019-11-29 11:54:53
问题 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:// URLs are not supported > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help > biocLite() BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2

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

由 假如想象 提交于 2019-11-29 02:52:19
问题 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 is my sample data ( df[1:2,] ): row.names organism gene 41 Homo-Sapiens ENSP00000335357 115 Homo-Sapiens ENSP00000227378 and I want to get something like this row.names organism gene id 41 Homo-Sapiens ENSP00000335357 CDKN3 115 Homo-Sapiens

differences in heatmap/clustering defaults in R (heatplot versus heatmap.2)?

由 痞子三分冷 提交于 2019-11-28 17:53:46
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 get both functions to give the same result (or highly similar result) so that I understand all the 'blackbox' parameters that go into this. This is the example data and packages: require(gplots) # made4 from bioconductor require(made4) data(khan) data <- as.matrix(khan$train[1:30,]) Clustering the data with heatmap.2 gives: heatmap.2(data, trace=

BioMart: Is there a way to easily change the species for all of my code?

由 时间秒杀一切 提交于 2019-11-28 11:18:48
问题 Below is a small fraction of my code: library(biomaRt) ensembl_hsapiens <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") hsapien_PC_genes <- getBM(attributes = c("ensembl_gene_id", "external_gene_name"), filters = "biotype", values = "protein_coding", mart = ensembl_hsapiens) paralogues[["hsapiens"]] <- getBM(attributes = c("external_gene_name", "hsapiens_paralog_associated_gene_name"), filters = "ensembl_gene_id", values = c(ensembl_gene_ID) , mart = ensembl_hsapiens) This bit of
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