Bioconductor Forum

Hi I just downloaded the latest version of R for Suse Linux 8.2 and I wanted to update all my bioconductor packages. I typed: getBioC(libName="default") And I got (finally) * DONE (reposTools) Loading required package...reposTools Loading required package: tools Error in Bundle(x) : No slot of name "Bundle" for this object of class "localPck". I must say that I dearly love the good ship Bio…

updated 21.1 years ago • michael watson IAH-C

TRUE, filters=filters, param=vcf.params, verbose=TRUE) starting filter filtering 1202 records Error in extractROWS(x, eval(filter, x)) : error in evaluating the argument 'i' in selecting a method for function 'extractROWS': Error...in eval(filter, x) : filter rule evaluated to inconsistent length:</pre> Moreover, the error changes depending on the order of the filters: <pre> …

variantannotation vcf filtervcf

updated 10.2 years ago • TimothéeFlutre

somebody tell me what is going on ??? Warning message: cannot open: HTTP status was `404 Not Found' Error in loadFromUrl(srcUrl) : URL http://www.genome.ucsc.edu/goldenPath/hg17/da tabase/refLink.txt.gz is incorrect or the...target site is not responding! Error in ABPkgBuilder(baseName = file.path(myDir, "AnnTh"), srcUrls = getSrcUrl( "ALL", : Failed to parse Golden Path data because of…

updated 21.6 years ago • Mayte Suarez-Farinas

Hello All, I am trying to analyze sc-RNA data using both scater and scran. While trying to run normalization using scran via the computeSumFactors...method, I get the following error. Could someone please explain me what this error means and if there a way to fix it? Appreciate all your help and suggestions...computeSumFactors(ScaterObject, sizes=c(20, 40, 60, 80)) summary(sizeFactors(ScaterObj…

scran scater

updated 9.0 years ago • hrishi27n

plot. I ve tried different bam file but always new() command is ok while each other give me this error: Error in intoNbins(gr, bcount) : all 'width(gr)' must be >= 'n' Why? Thank All

metagene

updated 9.6 years ago • arinaldi

Hi all, I just installed R 2.5 today and then installed Bioconductor 2.0 using the recommended biocLite(). I then tried to...Hi all, I just installed R 2.5 today and then installed Bioconductor 2.0 using the recommended biocLite(). I then tried to call...nbsp;duplicateCorrelation() from limma, but got this error: <pre> > corfit <- duplicateCorrelation(MA…

limma

updated 11.1 years ago • Jenny Drnevich

Hi all, I am using edgeR to identify genes differentially expressed in my experiment. I have cells which were grown in 4 different...cell media and I would like to perform an ANOVA to identify DE genes comparing all media vs all (e.g. media1 vs media2; media1 vs media3; media1 vs media4; media2 vs media3....). I have been reading the manual for edgeR...con) #Test on glm. Not filtered on FC …

edger error

updated 6.8 years ago • lucap

<div class="preformatted"> Dear all, Have tried using random forest for classfication and this is the code i wrote exactly: trial.rf<-randomForest(Type ~., data...div class="preformatted"> Dear all, Have tried using random forest for classfication and this is the code i wrote exactly: trial.rf<-randomForest(Type...Type is a column and determines the type and the tri…

updated 13.9 years ago • Salwa Eid

Hello all, Seem there is something wrong with my samples samples <- read.csv("samplesheet_DiffBind.csv") result <- dba.analyze...samples) Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator I understand what this error means but don't know

DiffBind ATACSeq

updated 2.8 years ago • Chris

div class="preformatted">Hi all, I got an error when I used predictCoding() in VariantAnnotation package. > coding <- predictCoding(vcf, txdb, injected_Arabi...Error in .Call2("DNAStringSet_translate", x, DNA_BASE_CODES, lkup, skipcode, : in 'x[[24606]]': not a base at pos 3 How can I get the value

updated 13.2 years ago • sun

div class="preformatted">Hi I have been getting an error in packages db family. First I was getting "Error in checkDBSCHEMA(dbconn, "GO_DB") : invalid DB schema version (found 2.0, expected...2.1)" I decided to reinstall R with version 2.10.1 and reinstall all packages again. still I have problems with GO. I reinstalled through the Package Manager and by using biocLite directly...It insta…

GO GO

updated 15.8 years ago • Mayte Suarez-Farinas

subnetwork displayed in Cytoscape select (node.names) selectFirstNeighbors () clear () # clears all current selections invert () # inverts the current selection hide () # hides selected nodes unhide () # reveals everything hidden...layout be applied; actual write.gml (filename) # save current graph to file render () # applies all visual mapping ('vizmap') rules, see below ---…

Visualization Network graph Visualization Network graph

updated 15.6 years ago • Paul Shannon

Hi, I analyzed scRNA-seq data. Using Seurat, we have an object with 19742genes in 2516 cells. In that, control group 525 cells, treatment group 1991 cells. by "FindMarkers" function I got the different gene expression matrix between the control (pct.1) and treatment (pct.2) groups. ``` >dim(mydata) [1] 540 2 >mydata[1:10,1:2] pct.1 pct.2 Fth1 0.996 1.000 Fosb 0.…

GSVA scRNA-seq data

updated 5.6 years ago • initialqy

camera(voom_data,all_signatures_for_camera,design,contrast.matrix1)</span></pre> I get the error Error in U\[iset, , drop = FALSE\] : no 'dimnames' attribute for array Here the voom\_data is the voom output, design is what i...use the design matrix in voom. all\_signatures\_for\_camera is a list of 18 gene sets? What is causing the error ? thanks

limma camera

updated 10.2 years ago • ea1402

find gRNAs and their off-targets in some sequences. For a couple of sequences, I got the following error message while the program was trying to find all hits in a particular sequence: "Error in .seqlengths\_TwoBitFile(x) : UCSC..._TwoBitFile(x) : End of file reading 4 bytes" Could you please tell me what the cause of this error message may be? Thanks, Joyce

crisprseek

updated 8.1 years ago • joyce

Hi all, I am new to Diffbind and following the workflow from the handbook: https://bioconductor.org/packages/devel/bioc/vignettes...Hi all, I am new to Diffbind and following the workflow from the handbook: https://bioconductor.org/packages/devel/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf I used HMMRATAC to generate the peak files, instead of MACS2. So I used the HMMRATAC output .summit (…

peakfiles diffbind HMMRATAC

updated 3.6 years ago • jonathanho1989

bam files of different breeds and while I can successfully run it by breed, when attempting to use all of them i get the following error: <span style="background-color:Yellow">Error in getReadCountsFromBAM(BAMFiles, refSeqName...files and they are different, however i dont know how to change them in order to look alike and run all of them together. Some of the bam files have been downloade…

cn.mops

updated 7.4 years ago • laurabuggiotti

Thank you very much Dario for help. When i try using loadAllData in deepSNV package ,i got an error. below is script and error: #===================== library("TxDb.Hsapiens.UCSC.hg19.knownGene") txdb<-TxDb.Hsapiens.UCSC.hg19.knownGene...1] files<-c("test.sorted.bam","control.sorted.bam") counts<-loadAllData(files,gr,q=10) #------------------ Error in unlist(sapply(1:…

deepSNV deepSNV

updated 11.5 years ago • Asma rabe

div class="preformatted">Bioconductors- I have produced the following error upon calling hyperGTest with several different datasets. I have reproduced the error below using data from the ALL...code parsed from the GOStats vignette. Any help would be appreciated. Cheers, -Casey > data(ALL, package = "ALL") > Bcell <- grep("^B", as.character(ALL$BT)) > subsetT…

GO hgu95av2 GOstats GO hgu95av2 GOstats

updated 17.7 years ago • Christopher Brown

<div class="preformatted">Dear BioC, How can I install all metaData available (including CDF,Probe and Annotation) information from URL: http://www.bioconductor.org/packages/data...div class="preformatted">Dear BioC, How can I install all metaData available (including CDF,Probe and Annotation) information from URL: http://www.bioconductor.org/packages...annotation/stable/src/contri b…

cdf cdf

updated 20.6 years ago • SAURIN

Dear All, Greetings for the day!! When I running CexoR, I am facing below error. Error in if (C != 0 && D != 0) { : missing value where TRUE/FALSE...rep1,rep2,rep3), chrN="chr1", chrL=249250621, idr=0.01, p=1e-12, N=3e4). I am clueless about above error. can anyone please help me to solve the issue.   Best Regards, Sudhir  &nbsp

CexoR

updated 8.4 years ago • sudhirjadhao2009

div class="preformatted">Dear All, I am trying to use DiffBind and having an error. The data set is just two conditions without any replicates. I set up the contrast...manually as groups as suggested.I get the error in dba.analyze step. Here is the actual commands and the error I get: > tamoxifen = dba(sampleSheet="~/Data/NYU/Michael/Marcus...tamoxifen$masks$Dex, tamoxifen$masks$BDNFD…

DiffBind DiffBind

updated 12.1 years ago • Kasthuri Kannan

Dear all, when I use this function:  simbols.eg <- select(Homo.sapiens,keys=elementMetadata(genes.gr)$gene\_id,columns="SYMBOL...keytype="GENEID") I get this error: Error in UseMethod("select\_") :    no applicable method for 'select\_' applied to an object of class "c('OrganismDb', 'MultiDb

homo.sapiens

updated 9.5 years ago • ribioinfo

r library("rpx") px1 <- PXDataset("PXD000001") Querying ProteomeXchange for PXD000001. Error in file(file, "rt") : cannot open the connection to 'ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/README.txt...a tutorial about Quantitative Proteomics using rpx to import data and PXDataset keeps giving me error in fpt connexion. Is there any way to load all needed data in…

PRIDE rpx PXDataset

updated 3.7 years ago • gianluigi.caltabiano

<div class="preformatted">Hello, I receive the following error message when trying to load the golubEsets library: > library(golubEsets) Error in open.connection(con, "rb") : unable to open connection In addition: Warning message: cannot open compressed file `C:/PROGRA~1/R/rw2000/library/golubEsets/data/golubTrain.rda' Error in library(golubEsets) : .First.lib failed for 'golubEset…

updated 21.2 years ago • Samantha Ying

I have a question. When I tried to install the development packages (by getBioC(develOK=TRUE) ) an error is generated that says : __________________________________________ [1] "Installing reposTools ..." Loading required...package: reposTools Loading required package: tools Error in getBioC(develOK = TRUE) : default: targets affy, cdna and exprs. exprs: packages Biobase, annota…

Biobase annotate genefilter reposTools affy Biobase annotate genefilter reposTools affy

updated 20.9 years ago • Tom Shi

to extract the pseudo amino acid composition using the __protr____ __package but I'm getting the error. here is the code : source("https://bioconductor.org/biocLite.R") biocLite("Biostrings") library(protr) testNeg_seq= readFASTA...C:/Users/Shreya Sarkar/Desktop/negativeboth.txt") ####check if there are 20 aa in all the seq check1_test = t(lapply(testNeg_seq, …

r source code error

updated 7.6 years ago • shreyasarkar0

value of grlB: (list $a, $b and dataframes for c,d) $a c d $b c d I have tried this to get all the combinations of the list but I get an error...     comb\_apply <- function(f,..., MoreArgs=list()){       exp <- unname...exp))     }     comb\_apply(countOverlaps,grlA,grlB)   &…

genomicranges mapply grangeslist

updated 10.2 years ago • francesca casalino

Bioconductor, I have installed R-1.9.1 on my AMD 64 remotely..! [ imp. remotely] i have installed all bioconductor pkgs except Rgraphviz and Rhdf5 !! I am running R scripts and..I have following errors : > library(tcltk,warn.conflicts...FALSE); Error in fun(...) : no display name and no $DISPLAY environment variable Error: .onLoad failed in loadNamespace Error in library(tcltk...gt; aba…

Cancer cdf rhdf5 Rgraphviz Cancer cdf rhdf5 Rgraphviz

updated 21.6 years ago • SAURIN

Hi all, I´m trying to follow ViSEAGO package tutorial (http://bioconductor.org/packages/devel/bioc/vignettes/ViSEAGO/inst/doc...ViSEAGO.html#references) and at point 3.2 I´m getting following error: BP_sResults<-ViSEAGO::merge_enrich_terms(Input=list(condition=c("BP","classic"))) Error in setnames(x, value) : Can't assign

go

updated 5.8 years ago • m.n

Hello All, I have 300 chIP peaksets. I am trying to count and analyze them using DiffBind. However when I am running the code, I get the...Hello All, I have 300 chIP peaksets. I am trying to count and analyze them using DiffBind. However when I am running the code, I get the following error. Will appreciate any suggestion to fix it. Many thanks. dba.count ... dba.parallel.lapply -&g…

DiffBind chip-seq differentially-binding-site

updated 5.3 years ago • Mar Mar

div class="preformatted">Hi All, I have a problem reading my cel files. My data is from Arabidopsis thaliana and the platform is GPL17417. I get the cdf file...GPL17417_aragene10st_At_TAIRG and installed it in R. But still when I read the cel files I get the error as follows: >affydata <- ReadAffy(cdfname="gpl17417aragene10stattairgcdf") Warning message: The affy package can…

Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps

updated 7.8 years ago • nooshin

https://rna.recount.bio), but when I fetch these datasets and load the counts, I get 0 counts for all samples! All the metadata columns do exist though. Here's the code I use to retrieve these: ``` library(recount3) ramakar = recount3...annotation = "gencode_v29", type = "gene" ) ramakar.exp <- assay(ramakar, "raw_counts") all(apply(apply(ramakar.exp, 2, functi…

recount

updated 2.4 years ago • urwah

<div class="preformatted">Dear all! I have 88 CEL files, and I'm about to do some initial quality control. Right now I just want to read in the raw data. I have a 64 bit...div class="preformatted">Dear all! I have 88 CEL files, and I'm about to do some initial quality control. Right now I just want to read in the raw data. I have a 64...set the wd to the same directory as my files, and…

updated 18.8 years ago • Boel Brynedal

I'm posting this error here to have a clearer idea of what's going on.  I'm running tximport using my own dataset and following and modifying...agrees with what I have in that directory and inside each sample folder. However, when I check if all files are listed, I get this error: _all(file.exists(files))_ _FALSE_ In my previous (misplaced) post on GitHub issues, I was

bioconductor tximport rnaseq R

updated 9.3 years ago • ctl

i86pc and Solaris 10 6/06 s10x_u2wos_09a X86. I have seen the help messages concerning memory errors but cannot find a solution to unix memory errors. I thought R would be using all available memory? I have 8Gb RAM and 4Gb...I am running one 500K test chip and when I try to create a SnpQSet in oligo I get the following error: Error: cannot allocate vector of size 1.8 Gb $ ulimit -a time(se…

oligo oligo

updated 18.6 years ago • Beth Wilmot

Hi all, Would you have a suggestion how to fix the error below? Thank you so much! if (!require("BiocManager", quietly = TRUE)) install.packages...BiocManager") BiocManager::install("csaw") library(csaw) Error in library(csaw) : there is no package called ‘csaw

ChIPSeq ATACSeq

updated 2.8 years ago • Chris

Hello all, I'm very new to all of this so please bear with me, but I'm trying to do some RNA-seq data analysis using DESeq2. I am attempting...design = ~ 1)</pre> But when I run the command I receive the following error: <pre> Error in round(assay(se)) : non-numeric argument to mathematical function</pre> From all the Googling I've done it seems...corresponding to sample co…

deseq2 R error

updated 7.8 years ago • jamesvsheppard

met a problem as some other met:   <pre> <span style="background-color:rgba(255, 255, 255, 0)">All gene-wise dispersion estimates are within 2 orders of magnitude from the minimum value, and so the standard curve fitting...techniques will not work.</span></pre>   I know the error is reported in DEseq2, and the solution post online is not available fo…

dexseq

updated 8.7 years ago • zhan0949

Hi all, I am using DMRcate to find differentially methylated regions in illumina 450k data between one group of 4 samples and...another group of 9 samples. I followed all the steps of DMRcate user's guide and I build the design matrix in a similar manner, and this is it: <pre> str(design) num [1:13, 1...type : chr "contr.treatment"</pre>   But when I call the c…

dmrcate design matrix

updated 10.2 years ago • Giovanni Calice

package for batch effect correction in microbiome data. Recently, I updated the package to resolve all errors caused by clashes with functions from the dependency packages. However, I continue to receive a check report for...BioC3.19 telling me the same previous error, which I believe I have already addressed. Could you kindly advise if there are any additional steps I may have overlooked

PLSDAbatch

updated 15 months ago • anjiwangyiwen

When I run `zlm` with several clusters (I have clusters 1-7), how to compare 1 cluster versus all the others? ``` zlmCond <- zlm(formula = ~leiden_r0.3 + n_genes, sca=sca, method = "glm") 1_vs_others <- summary(zlmCond, logFC = TRUE...When I run `zlm` with several clusters (I have clusters 1-7), how to compare 1 cluster versus all the others? ``` zlmCond <- zlm(formula =…

MAST

updated 4.5 years ago • Dan

div class="preformatted">Hi All, I'm playing around with KEGGGraph to examine some pathways, and I am running into some errors. When I try to plot some pathways...I get the error: "Error in .subtypeDisplay(object) : Given subtype 'missing interaction' is not found!" Here is an example with one pathway...that gives the error and another that does not: library(KEGGgraph) # this one gives t…

Pathways KEGGgraph Pathways KEGGgraph

updated 15.5 years ago • Robert M. Flight

s lmFit on a geo dataset pertaining to heart failure. Whenever I run the lm.fit command I get the error: Lm.fit() giving Error in lm.fit(design, t(M)) : incompatible dimension. I am trying to run the differential expression...contains the values yes (failing heart), no (non failing heart), NA. In my code I try to get rid of all the rows in the ESET that contain NA values . Here is my co…

limma differential expression design matrix error eset

updated 10.5 years ago • Vani

<div class="preformatted">Dear all, I am in trouble with pamr.knnimpute (library pamr) When I use this function in a "for" loop with matrix of 4 samples at each loop...div class="preformatted">Dear all, I am in trouble with pamr.knnimpute (library pamr) When I use this function in a "for" loop with matrix of 4 samples at each...R does a segmentation fault which ends with a fatal er…

pamr pamr

updated 20.7 years ago • Alice Le Bars

Hi all, I try to run FindConservedMarkers() but I got this message: ```r markers_cluster_8 <- FindConservedMarkers(CV.harmony...Hi all, I try to run FindConservedMarkers() but I got this message: ```r markers_cluster_8 <- FindConservedMarkers(CV.harmony, ident.1...8 not present in group A. Skipping NCError in marker.test[[i]] : subscript out of…

seurat

updated 2.9 years ago • Chris

Hi, I'm using DEVis for differential expression analysis. When I get to running DESeq I get an error about "object of class “NULL” is not valid" when I'm creating the aggregated data. running BiocManager::valid() returns [1] TRUE...NA 3996 0.1218624 0.00000 4.06264 0.000000 1.00000 NA #Make a list of all of our contrasts. result_list <- list(res.SAMP…

DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis

updated 3.6 years ago • Ana

<div class="preformatted">Dear all, I am quite new to the "affymetrix normalization data world" and until now, I was always normalizing my data using the good old RMA method. People in the wet lab I am collaborating with asked me to renormalize a set of data coming from different labs and I discovered the fRMA method which is certainly more suitable in that case. I am working on the mous…

Normalization frma Normalization frma

updated 14.3 years ago • SylvainBrohée

pre> Hi, I am using ""metagene" to plot average reads signal around gene, but it gave error like this: Error in intoNbins(gr, bcount) : all 'width(gr)' must be >= 'n'.</pre> My command is : <pre> mg <- metagene$new(genes, "H3K4me3.bam...cores = 8, force_seqlevels = TRUE)</pre> After add the parameter of  "bin\_count=30", <pre> Error in .…

metagene metagene$new

updated 8.1 years ago • Wojeff

div class="preformatted">Hi all, I'm trying out the vsn procedure instead of rma. But i got the following error message. What does "ARG" mean? Must the VSN procedure...saying that "multiget is deprecated? I installed the R vers.1.9.0 and BioC 1.4. I appreciate all the help that you can give me, Edmund > eset <- expresso(Data, bgcorrect.method = "mas", normalize.method = "vsn",…

vsn vsn

updated 21.6 years ago • echang4@life.uiuc.edu

analysis on ChIP-seq data, comparing two groups with 3 replicates for each. I am now facing an error when using its dba.count function. I created a DBA object, Expt, using a sample sheet. Expt <- dba(sampleSheet=”Expt.csv...function as follows. Expt <- dba.count(Expt, peaks=Expt$masks$Consensus) I then got an error message as follows. Error in pv.counts(DBA, peaks = peaks, minO…

diffbind

updated 9.5 years ago • shohei.hori

div class="preformatted"> Hello all, I am trying to map a set of Genbank accession numbers to LocusLink IDs and get the following error using humanLLMappingsACCNUM2ALL...gt; get("AF426250",humanLLMappingsACCNUM2LL) Error in get("AF426250", humanLLMappingsACCNUM2LL) : recursive default argument reference I can map the other way from locuslink

updated 20.9 years ago • Denise Scholtens

Hi all, So I got several bed files as created by MACS2. I am loading them as list with the following: peaks <- as.list(c("K002000291_97925.narrowPeak...GSM1174481_ARmo_1nM_peaks.bed.gz" but when I convert them to the GRanges I got the following error: peak=readPeakFile(peaks) Error in read.table(file = file, header = header, sep = sep, quote = quote, : 'fil…

ChIPseeker readPeakFile

updated 6.7 years ago • theodore.georgomanolis

<div class="preformatted">Hi all, I have a problem when installing the R-package VariantAnnotation, I get the following error message: Error : object ?get_xsbasetypes_conversion_lookup? is not exported by 'namespace:Biostrings' ERROR: lazy loading failed for package GenomicFeatures * removing /home/als/R/x86_64-unknown-linux-gnu- library/2.15/GenomicFeatures There have been several r…

VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation

updated 12.6 years ago • Thomas Damm Als

pH, disease status etc. I know I can give them as new columns in sample sheet, but are there proper rules to do that? For example, some columns will be integers, some will be characters, some will be categoricals, etc. And I want...to control for all those covariates and perform differential binding analysis between control vs disease. Here is my knowledge on this...with linear modelling, and put…

DiffBind Deseq2

updated 5.2 years ago • bioinfouser2

Dear All, I was trying to use ELMER package with some different TCGA tumor types in order to study enhancers. I had no problems with...when I use another TCGA cancer type (GBM) with the default pipeline TCGA.pipe I get the following error: Error in (function (mee, probes, nearGenes, percentage = 0.2, permu.size = 10000,  :  Probes option should be subset of...row names of meth…

software error ELMER

updated 9.7 years ago • mcastrod

div class="preformatted">Hi BioC, Can any one tell what could be the reason for this error: myGOCC <- GOHyperG(myUNQLL, lib="moe430a", what="CC"); GOLocmap<-mget(names(myGOCC$intCounts),GOALLLOCUSID); Error in mget...names(myGOCC$intCounts), GOALLLOCUSID) : Object "GOALLLOCUSID" not found I am trying to get ALL LocusIDs accociated with GO terms. I don't know why I am…

updated 21.3 years ago • SAURIN

Hi all, I am attempting to run DEXSEQ on a large number of samples (100+) but I am receiving the following error message. I believe it...might be at the estimateDispersions step. "Error in names(res) <- nms : 'names' attribute [16] must be the same length as the vector [1] Calls: estimateDispersions ... estimateDispersions

software error

updated 5.5 years ago • huck.thornton

Sir, While running DEXSeq on a Human dataset, (commands given below), I get the following error. <code>> countFiles=list.files(inDir,pattern="fb.txt$",full.names=TRUE)<br/> >flattenedFile=list.files(inDir,pattern...gt;dxd_ed=estimateDispersions(dxd_esf,fitType="mean") `` <pre> #using supplied model matrix #Error in estimateDispersionsFit(object, fitType = fit…

DEXSeq estimateDispersions

updated 11.1 years ago • deeya.saha86

Dear all, I have been running an example a tutorial for proteome data analysis and I could not load the package shinyTandem. I got...the following error message: "Error in library("shinyTANDEM") : there is no package called ‘shinyTANDEM’" I would highly appreciate if you can help

software error proteomics

updated 6.8 years ago • pdaltron