Bioconductor Forum

Hello, I'm looking at objects generated using the previous version of SomaticSignatures in the latest version.  The objects were generated as part of the example in the vignette...samples’ for signature ‘"list"’</pre> Some of my own data objects I generated using the previous version (which functioned correctly) are also throwing similar errors when I try to use some of the plot …

somaticsignatures

updated 11.1 years ago • Dave Wettmann

a single-cell RNA seq experiment (even after filtering to exclude genes with low and very high count numbers) the data range returned from a DESeq2 rlog transformation appears dependent upon the number of samples: <img alt="" src

deseq2 rlog

updated 10.6 years ago • snsansom

between these two normalization units, especially given that I used `diff.method="edgeR"` to identify DMRs. Also note, I am familiar with the fact that deeptools can generate bigwig directly from the BAM, and while they...provide a number of normalization methods with their `bamCoverage` function, I would still prefer to use the normalized counts from

MEDIPS

updated 4.8 years ago • lshepard

a second method of using the likelihood ratio test, followed by a clustering tool (degPatterns) to identify genes following a specific expression pattern (i.e., knockdown < control < overexpression). The number of significant

DESeq2 DifferentialExpression

updated 4.7 years ago • Matt

Hello, I'm trying to return to a previous version of edgeR (3.26.1). I had been using edgeR 3.26.1 and R 3.6.0 within a bioinformatics pipeline implemented on a supercomputing...e.g., edgeR 3.26.1). I've been able to install R 3.6.0 again, but the compatible Bioconductor version (3.9) only lets me go back to edgeR 3.26.8. Running my analysis with edgeR 3.26.8 also gives different DE result…

edgeR Bioconductor

updated 4.2 years ago • mvanhorn

div class="preformatted">dear all, The package installation for the R version 2.4 on our Linux server stopped - apparently because of an outdated version of affy (see error message below). A more general...our frequent questions about adding or updating packages, and also with the dependencies between versions of the different packages. I thought to apply BiocLite more routinely now that we …

affy affy

updated 18.9 years ago • Talloen, Willem [PRDBE]

Hello, I tried to install the package PhyloProfile via RStudio and Terminal using: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("PhyloProfile") Bioconductor version 3.9 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Installing package(s) 'PhyloProfile' Installation path not writeable, una…

PhyloProfile

updated 6.0 years ago • hansd286

I would like to analyze. I have four conditions (Control, MutA, MutB, MutA+B) and my aim is to i) Identify which phosphosites are behaving differently across time in the double mutatant (MutA+B) when compare to MutA and...using splines (9.6.2) possible given that I only have 3 time points? - how to select the correct number of dfs? - Should I use `duplicateCorrelation` since the same replic…

limma splines

updated 3.9 years ago • rina

Is the package ‘airway’ not available for R version 3.2.2?  I tried to install it and I got this answer: BioC\_mirror: http://bioconductor.org Using Bioconductor version...2.14 (BiocInstaller 1.14.3), R   version 3.2.2. Installing package(s) 'airway' Warning messages: 1: package ‘airway’ is not available (for R version 3.2.2) Is it not

airway

updated 10.1 years ago • jmmonroykuhn

if it is even possible to perform differential exon usage analysis with DEXSeq having a large number of samples, in my case almost 600? Samples are unequally divided between two conditions (1:10 ratio) and DEXSeq object

dexseq estimatedispersions

updated 7.4 years ago • nemanja.vucic

In total: about 18000 transcripts, 5 time points, 2 genotypes. What I want to achieve: I want to identify all transcripts/genes with different kinetic trends in two genotypes. For example, gene A is stable from t1-t3 and

RNASeqData DESeq2 DifferentialExpression

updated 18 months ago • ZhuYi

Hi all! I was puzzled by an error message I got in `` Gviz `` adding an `` AlignmentsTrack `` representing RNA-seq data: <pre> Error in .Call(.NAME, ..., PACKAGE = PACKAGE) : negative length vectors are not allowed</pre> After looking through some code and testing stuff I got to the root of the problem, the `` sequenceLayer `` function in `` GenomicAlignments ``. To me it looks…

genomicalignments c gviz

updated 10.0 years ago • Johannes Rainer

example you give in the BMC Bioinformatics paper. We were wondering how to import large or entire numbers of probesets into the myPS object? It may be a basic R command, but unfortunately we rely on commercial software for...list (set it as the myPS object) to pull out the Illumina Probe ID using the refseq column as the identifier column. We can export all these with a simple write command…

probe annotationTools probe annotationTools

updated 16.3 years ago • Yingfang Tian

I would like to process proprietary RNA-Seq data with the same version of the pipeline behind recount3 data ([Monorail][1]). To do so, I downloaded the latest stable versions of [recount-pump][2...unify][3] (v 1.1.1), as suggested in the Monorail github repo. Now, I would like to retrieve the version of the Monorail pipeline used to generate TCGA data available on Recount3 R package, so tha…

recount3

updated 2.2 years ago • Lorenzo

div class="preformatted">Dear all, I want to estimate copy number values for a set of ~200 samples (100 paired Tumor and Normal mucosa). Do I need to tell CRLMM that I have "normal/germline...samples (with an expected average copy number of 2) and tumor samples (which may hay many genomic alterations). Furthermore, is it useful/do I need to specify the N-T paired

crlmm crlmm

updated 14.6 years ago • Sole Acha, Xavi

according to http://bioconductor.org/packages/devel/bioc/html/recount.html), I installed the latest version of R (3.3.1) and then tries installing recount, but, unfortunately, it doesn't work: <pre> > biocLite("recount") BioC_mirror...http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.3.1. Temporarily using Bioconductor version 3.0 Instal…

recount

updated 9.3 years ago • arjunkrish

chooseTopHubInEachModule can be used to identify the top hub gene in each module. May I know how to obtain the summary of how many genes each gene connected in the same

connected

updated 3.8 years ago • wes

CNV). I have the cell files from Affymetrix 6.0. I appreciate your help [[alternative HTML version deleted]] </div

updated 15.6 years ago • Kay Jaja

Two-Class Unpaired Case Assuming Unequal Variances s0 = 0.0122 (The 0 % quantile of the s values.) Number of permutations: 100 MEAN number of falsely called genes is computed. Delta: 0.5 cutlow: -Inf cutup: 4.25703 p0: 1 Significant...Genes: 1 Falsely Called Genes: 0.19 FDR: 0.19 Error in mat.sig[, "d.value"] : incorrect number of dimensions The length of vector cl_0 equa…

updated 20.3 years ago • Heike Pospisil

answer, I'm fine with it, but I'm concerned that I'm doing something wrong. What are the ranges of numbers of differentially expressed genes that one would expect from DESeq2 or EdgeR? More information: I'm in the midst of

Genetics edgeR DESeq2 Genetics edgeR DESeq2

updated 11.4 years ago • Jessica Perry Hekman

BeadChips, but the hybridisation seems to have been done in several batches, with different numbers of probes in each batch, alternating between 48803 and 48804. Can anyone tell me how to combine these different batches...the matrices are not the same length (precise error is "Error in cbind(out$E, objects[[i]]$E) : number of rows of matrices must match (see arg 2)"). Thank you in advance, Gavi…

probe limma ArrayExpress probe limma ArrayExpress

updated 14.6 years ago • Gavin Koh

Hello! I am currently setting up a pipeline for RNAseq data analysis to identify differentially expressed genes (DEG) using DESeq2. I am trying to validate the results of my pipeline with previously...published experiments but I dont seem to find any papers using the current version of DESeq2 (v1.30.0) with available reads. I found that installing previous versions of DESeq2 can be troublesom…

DESeq2

updated 4.9 years ago • Samuel Daniel

I recently updated my package Logolas in Bioc 3.7 (R 3,5) version. While that version works fine, a few of my R users complained that the Bioc 3.6 ( R 3.4) version is now broken. I want to change...the Bioc 3.6 version as well or at the least direct users to Bioc 3.7 somehow. What route should I take?   Thanks   Kushal   &nbsp

Logolas old-version BiocUpgrade

updated 7.6 years ago • Kushal K Dey

<div class="preformatted">Dear Mamun: Your code looks ok. I would suggest you do some quality checking for your raw data. For example, you can use boxplot to show the intensity distribution for each arrays and visually inspect the difference between your arrays. You have got quite a few arrays which should come from different chips. It might be worthwhile to check if their is a chip ef…

Microarray Normalization probe limma lumi Microarray Normalization probe limma lumi

updated 16.3 years ago • Wei Shi

from ensemble release 73 is required. I was wondering if had any plans on supporting different versions of ensembl's variant_effect_predictor.pl script with your ensemblVEP package. As far as I know, ensembl is on a...update less frequently than ensembl itself, relying on previous ensembl and variant_effect_predictor versions. For example, we are currently still using the database schemas and t…

ensemblVEP ensemblVEP

updated 12.2 years ago • Guest User

of R (3.1) and therefore this prevents me from using the development version of Bioconductor (2.14). Is that right? I dont particularly want to use an unstable version of R. Can I get the development...version of Bioconductor without having to use the development version of R? My R session is pasted below. Kristina R version...version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. > useD…

GUI DESeq2 GUI DESeq2

updated 11.9 years ago • Kristina M Fontanez

Hi everyone, I'm wondering where could I find the number of protein-coding genes in each chromosome arm in human? I have searched the ensembl, but it only gives the the number

gene chromosome proteincodinggene

updated 2.6 years ago • Liliian

Hello, I am using the copy number data from the TCGA to observe focal and broad copy number events. After downloading the CNA data I noticed the segmentation

segmentation reference CNA TCGA

updated 6.8 years ago • jlarsen728

Hello, I am new to using R and bioconductor, so I apologize for any errors. What I am trying to do is use the msigdb database to retrieve the KEGG gmt data for a GSEA analysis and convert the human genes to zebrafish genes. I followed a previous posts on how to retrieve the data online and in their case they converted the human KEGG gene symbol identifiers to human ENSEMBL codes. I tried to re…

msigdb gmt GSEA

updated 20 months ago • Georg

if I am misunderstanding the consensus peak.  I am under the impression that this is the number of peaks contained within a set.  for example all peaks in control replicates.  When using overlap the last...number matches my venndiagram, but when added the consensus peak to my set it does not:   <pre> dba.overlap(test,test$masks...het 1-2-3 ma…

diffbind

updated 8.8 years ago • cperez5

I installed the latest R version 4.1.2, but I got problems with installing the latest bioconductor version 3.14. I can not install any package by bioconductor...I installed the latest R version 4.1.2, but I got problems with installing the latest bioconductor version 3.14. I can not install any package by bioconductor. Can anyone tell me the reason? THANKS! ```r > if (!requireNamespace…

Bioconductor

updated 4.0 years ago • Evan

CummeRbund") Warning in install.packages : package ‘CummeRbund’ is not available (for R version 3.2.3)</pre> When I went to the repository (http://compbio.mit.edu/cummeRbund/) it looks like it has not been updated since

cummerbund rstudio

updated 9.9 years ago • lreiter

hg18, or otherwise the IlluminaHumanMethylation450kCHR36 should not be supported. I am referring to version 1.4.6 of the IlluminaHumanMethylation450k.db package. -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics

updated 14.1 years ago • Dario Strbenac

lt;-"snp129" getTable(todo) ####====================== my question is how to retrieve data using identifiers(names/accessions). for example, is it possible to retrieve chromosome position given the rs number of several

rtracklayer rtracklayer

updated 16.4 years ago • li lilingdu

lt;-"snp129" getTable(todo) ####====================== my question is how to retrieve data using identifiers(names/accessions). for example, is it possible to retrieve chromosome position given the rs number of several

rtracklayer rtracklayer

updated 16.4 years ago • li lilingdu

data/metaData-devel/" [1] "Download complete." [1] "Installing mgu74av2" Note: Running R version 2.0.0 and package mgu74av2 was built for R version 1.9.0 , installing anyway. [1] "Installation complete" From URL: http...www.bioconductor.org/data/metaData-devel/ mgu74av2 version 1.6.2 ------------------------------ I can't understand why R does not download the version 2.0.0 of the…

mgu74av2 mgu74av2

updated 21.3 years ago • Florence Combes

div class="preformatted">Dear list: On the Windows version one can bring back R command history at the prompt by using a up-ward arrow key. Unfortunately I can not do the same thing...can set up the history function or command editing function, what ever you call that, with the unix version of R? Thanks in advance! Jianping xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Jianping Jin Ph.D. …

updated 19.5 years ago • Jianping Jin

Hello, We have a new problem when using version 4.12.0 with the opening command:     opening\_img = opening(mat\_bin, kern) The mat\_bin includes binary information...but also NA to delineate the area of interest (border). With the previous versions, 4.8.3 and 4.10.1, the NA were correctly handled. Using version 4.12.0, the resulting image shows unexpected border...…

ebimage

updated 9.9 years ago • jean.luc.lablee

preformatted">Hello, I am processing some CEL files using MAS5. I had processed them using earlier version of R(R1.6.1) and Bioconductor. The results I am getting for the same data with R 1.7 and new version of Bioconductor are...very different. The new version of bioconductor is running on Linux while the old version of bioconductor is running on Windows. It would be nice if

updated 22.4 years ago • Tapan Mehta

emptyValue = FALSE``` in the call to ```read.FCS```. Even so, a complaint is raised about an uneven number of tokens and the last keyword being dropped (see below). While this does not (as far as I noticed) impact the downstream...set emptyValue to FALSE and try again! > > read.FCS("test.fcs", emptyValue=FALSE) uneven number of tokens: 333 The last keyword is dropped. uneven nu…

flowCore

updated 6.7 years ago • OT

Hi, I am using the Bioconductor package BindingSiteFinder. However I want to use the latest version on BindingSiteFinder. I updated BiocManager to version 3.14 and also updated all packages (apart from Matrix for...some reason). Still der BindingSiteFinder version is [Package BindingSiteFinder version 1.0.0 Index], while on the webpage it says the version that goes with Bioconductor...packages/r…

Versions Update BindingSiteFinder

updated 2.9 years ago • M.Klostermann

am using SomaticSignatures package for data analysis. If I have four cancers under study should the number of samples for each cancer type be the same. I mean to ask that is this alright if for one cancer type I have

somaticsignatures

updated 9.4 years ago • arsala521

Hello, I want to compare gene expression against copy number variation at gene level in a TCGA project. when I retrieve the gene expression every value is mapped by sample and gene...But for the copy number variation, I get only chromosomal locations. To do the PCA, I want to have a table with gene, expression by sample, CNV by...lt;- GDCquery(project = "TCGA-GBM", …

TCGAbiolinks biomaRt

updated 2.5 years ago • Will Yam

I want to project the identified tophits genes(RNA-Seq) and proteins(proteomics MS/MS) onto a network of protein-protein interaction dbase

ppi network analysis igraph

updated 9.5 years ago • Abhishek Pratap

div class="preformatted">My sys admin won't install ImageMagick past version 6.2.8, which is apparently stock for RedHat in my company, therefore making it difficult to install EBImage. I am wanting...to use bwlabel in EBImage as an object identifier for a 2D binary image. Is there a work around for this or another known package that performs a similar function...as bwlabel in the R world? …

EBImage EBImage

updated 13.3 years ago • Brian Pettegrew

I don't have an experienced bioinformatician to work with. Recently I updated my Bioconductor version to "3.13" . But I can install packagespackage "blockwiseModules" by BiocManager::install(). Please see the error message...replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing pac…

Bioconductor

updated 4.3 years ago • orchidsinvalley

but there are 390 > pathways according to pathway2name. I'm wondering why these two > numbers are not the same. > >> library(KEGG.db) >> pathway2gene=dbGetQuery(KEGG_dbconn(), "SELECT * FROM pathway2gene") &gt...gt;> length(unique(pathway2name$path_id)) > [1] 390 > >> sessionInfo() > R version 2.13.0 (2…

Pathways Pathways

updated 14.1 years ago • Marc Carlson

bit new to deseq2's methods of normalisation and i observed that depending on the design formula the number of total genes differs, can someone explain the reasoning behind, thank you in advance

DESeq2

updated 4.5 years ago • Mohamed Malek

a bit. I'm about to launch into another AMI-based project, however, and I noticed that the AMI is R version 2.15.0, which is problematic because I need to run Rcpp and need a couple of packages (e.g,. forecast) that use Rcpp, which...need to be reconfigured. Just thought I'd ask first. Thanks! Jeff [[alternative HTML version deleted]] </div

updated 13.4 years ago • Jeff Knisley

several of those answers, questions remain almost the same. The main question is regarding the number of genes probed in this platform. According to Affymetrix Data sheet on this platform there are 764,885 distinct probes...to relevant literature on the reasons for these differences). However, with affy it automatically identifies the correct annotation file (at least the name *hugene10stv1*…

Microarray Annotation PROcess xps Microarray Annotation PROcess xps

updated 13.9 years ago • Azby Cdex

to install DESeq2 but I had problem and it didn't work. An error tells me I need to upgrade my R version. but unfortunately every time I reinstall R it was 4.1.2 version, not 4.2.1. my operation system is Ubuntu 22.04 LTS...using this command I tried to install R version 4.2 but after installation it was 4.1.2 sudo apt install -y --no-install-recommends software-properties-common dirmngr...proje…

DESeq2

updated 3.1 years ago • yari.hadi

it's an appropriate question for Bioconductor. Is there a place to find a list of housekeeping genes (identified by Affy)? Thanks, -Jack [[alternative HTML version deleted]] </div

updated 12.6 years ago • Jack Luo

div class="preformatted">Hi, I am working with some R scripts that seem to call the older version of affy (maybe 1.0) and R 1.5.1. When upgrading the affy package to 1.1, I seem to have lost the ability to run older R scripts...that use the affy 1.0 version. Is there an archive of R and affy that would allow users to keep using some of these older programs for scripts that...are written specif…

affy affy

updated 23.0 years ago • Vawter, Marquis

lt; * Connection #0 to host bioconductor.org left intact Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install Execution...sw_vers ProductName: Mac OS X ProductVersion: 10.14.6 BuildVersion: 18G87 R version (brew installed) R: stable 3.6.1 (bottled) Software environment for statist…

software error

updated 6.3 years ago • Aki Hoji

to empty droplets. [Link to manual.][1] Based on this, I thought that if I specified small number for lower, it will detect more non-empty cells and if used bigger number for lower, it will detect less non-empty cells...it didn't. In fact it is consistently detect more non-empty cells when lower is set to larger number. Am I missing something? Here is the code to reproduce the results. …

DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling

updated 5.1 years ago • C T

olap.rate [1] 17534 17534 17534 17534 17534</pre> for some reason I get the same number of peaks for each replicate/treatment... when I use plotVenn  <pre> dba.plotVenn(k4 ,k4$masks$Consensus & k4$masks...WT)</pre> I get different numbers for each replicate. Don't know if it matters but I have duplicated peaks in my BED file (with different scores). Ho…

diffbind dba.overlap

updated 9.8 years ago • Udi Landau

a process around the installation of R and Bioconductor with a known set of packages at specific versions for the purpose of long term reproducibility. We use sessionInfo to capture all the package versions. How can I find...in the Bioconductor archives a specific version of a package? For example, where can I find 'annotate\_1.42.0'? Thanks. --Bob   &nbsp

reproducibility archive source code

updated 10.1 years ago • brucbruc

I've tried both suppressMessages and suppressStartUpMessages with no success. "Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help A new version of Bioconductor is available after installing the most...recent   version of R; see http://bioconductor.org/install

package

updated 7.8 years ago • nick

but <pre> > biocLite("TCGAbiolinks") BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.0. Installing package(s) 'TCGAbiolinks' Warning message: package ‘TCGAbiolinks...is not available (for R version 3.2.0)</pre> anyone can help me, many thanks

software error TCGAbiolinks

updated 9.9 years ago • yizhong2md

<div class="preformatted">Hello, I am trying to use goseq to find enriched GO terms for zebrafish RNA- seq data and am looking for advice on manually providing gene length information and GO annotation to goseq. My RNA-Seq data is mapped to danRer7 Ensembl gene id's. Unfortunately danRer7 does not appear to be supported by goeqs's built-ins for ensembl gene ids. > supportedGen…

Annotation GO zebrafish goseq Annotation GO zebrafish goseq

updated 13.3 years ago • Ravi Karra