bioconductor

问题 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

问题 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 <-

问题 How do you find the overlapping coordinates and extract the respective seg.mean values for the overlapping region? data1 Rl pValue chr start end CNA 2 2.594433 6 129740000 129780000 gain 2 3.941399 6 130080000 130380000 gain 1 1.992114 10 80900000 81100000 gain 1 7.175750 16 44780000 44920000 gain data2 ID chrom loc.start loc.end num.mark seg.mean 8410 6 129750000 129760000 8430 0.0039 8410 10 80907000 81000000 5 -1.7738 8410 16 44790000 44910000 12 0.0110 dataoutput Rl pValue chr start end

问题 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 doesn't seem to be the most memory-intensive function compared to the other functions in this package (with the data I am analyzing). I do understand that there are other questions like this on Stackoverflow, but they all suggest to switch over to the 64

问题 In bioinformatics/microbial ecology literature a fairly common practice is to concatenate multiple sequence alignments of multiple genes prior to building phylogenetic trees. In R terminology it may be clearer to say 'merge' these sequences by the organism they came from, but I'm sure examples are better. Say these are two multiple sequence alignments. library(Biostrings) set1<-AAStringSet(c("IVR", "RDG", "LKS")) names(set1)<-paste("org", 1:3, sep="_") set2<-AAStringSet(c("VRT", "RKG", "AST")

问题 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

问题 This question already has answers here : How should I deal with “package 'xxx' is not available (for R version x.y.z)” warning? (15 answers) Closed 4 years ago . I'm trying to install GeneR library (http://www.bioconductor.org/packages/release/bioc/html/GeneR.html): I'm using win7 and the newest R 2.14.2. Error during installation: > source("http://bioconductor.org/biocLite.R") trying URL 'http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2.14/BiocInstaller_1.2.1.zip' Content

问题 Hope somebody could help me .. I'm trying to install the mzmatch.R package for metabolomics, following the instructions here: http://mzmatch.sourceforge.net/tutorial.mzmatch.r.php I'm completely new to R so this is my first time doing this sort of thing. First, I downloaded the latest version of R and installed it on Mac OSX 10.7. This is the version of R that I have running: R 2.15.0 GUI 1.51 Leopard build 64-bit (6148) Then I launched R64.app and typed the following commands (as specified

问题 I'm trying to use the mclust method on an .FCS format file (which is a flow cytometry format file) and I read this file into R as flowFrame object. install.packages("openCyto") # since the old version sefaulted my R session library( openCyto ) library( flowCore) library( mclust) trial1=read.FCS("export_Alcina TregMAIT_AV 10-1974 P1_CD4.fcs") a=as.matrix(trial1) Editors note: some of these are Bioconductor packages and you should install according to the help pages for that environment.

问题 I am trying to update 7 datasets within 1 group in an hdf5 file, but the updated datasets have different size dimensions than the originals (but the same dimensionality, ie 1D, 2D, and 3D). Is there a way to alter the dimension property in order to update the dataset? Alternatively, can I delete the previous group, and then create a new group in it's place? I'd rather not rebuild the entire h5 file (create file, create groups, create datasets) since it's decently complex. I am using the