Bioconductor Forum

Hi all, My package was compiled without any problems until this happened yesterday: http://bioconductor.org/checkResults...release/bioc-LATEST/sincell/ Summarising, there are 2 types of error: 1. In Linux and Mac: <pre> ... No methods found in "BiocGenerics" for requests: as.vector, unlist Quitting from lines 170-185 (sincell...vignette.Rnw) Error: processing v…

build report

updated 9.4 years ago • Miguel Juliá

<div class="preformatted">Dear List, I am getting a couple of erros when trying to import gpr files using the read.maimages of Limma RG1<-read.maimages(targets1,source="genepix") Error in sub(pattern, replacement, x, ignore.case, extended, fixed, useBytes) : input string 1 is invalid in this locale In this case I simply cannot load the corresponding gpr files > f…

updated 18.1 years ago • Ana Conesa

Hello all, I tried to load my count matrix with this command: DESeqObj <- DESeqDataSetFromMatrix(countData = RoundedReadCount...Hello all, I tried to load my count matrix with this command: DESeqObj <- DESeqDataSetFromMatrix(countData = RoundedReadCount,colData...metadata,design = ~ Condition) After that, I got an error like this: <pre> converting co…

deseq2

updated 10.6 years ago • bharata1803

Tissue". There is a column named Tissue in my phenoData of the eset. But it still gives me an error saying the elements of intgroup do not match the column names of the pData(eset). I don't know what wrong I am doing. Can anybody...suggest anything. Thank You. -- output of sessionInfo(): Error in prepData(expressionset,intgroup=intgroup): all elements of 'intgroup' should match column names o…

updated 13.6 years ago • Guest User

of differentially-expressed genes, colleagues ask to see the raw expression data, sometimes for all replicates.   We usually show the counts-per-million of the fitted data: eg. `` class(y)[1]     &nbsp...fit <- glmFit(y, design, …) `` `` cpm(fit$fitted.values) `` These values are the same for all replicates of given samp…

edger standard error glmfit

updated 9.6 years ago • david.hughes

hi, I am trying to install ShortRead package but after installation it says ' Update all/some/none? [a/s/n]: ' and after that I am unable to do anything not even simple functions. how can I solve this problem? your help...hi, I am trying to install ShortRead package but after installation it says ' Update all/some/none? [a/s/n]: ' and after that I am unable to do anything not even simple func…

software error

updated 6.0 years ago • ayeshakaramat

div class="preformatted">Dear all, I have been trying to install some packages and I am receiving the following error message: trying URL 'http://bioconductor.org...packages/2.1/bioc/src/contrib/annaffy_1.10.0. tar.gz' Error in download.file(url, destfile, method, mode = "wb") : cannot open URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib

updated 18.3 years ago • Fabio Passetti

Hi All, I am trying to read an idat file from an Illumina genotyping array that uses VeraCode microbeads technology. This is my...code and the error I get: <pre> <span style="background-color:rgb(225, 226, 229)">> library(illuminaio) > idat <- readIDAT("E:/Ck01EC032-VBP_R001_C001_GRN.idat...Error in idx[i, 1] : subscript out of bounds > sessionInfo()…

illuminaio idat

updated 10.9 years ago • lacion

<div class="preformatted">Hi all i am using the following command to do clustering using hopach ....and getting the following error .... eset.s is a matirx containing genes filtered through a ttest ... my data contains 3 treatments and 3 controls > gene.dist <- distancematrix(eset.s, d="cosangle") > dim(gene.dist) [1] 112 112 > gene.hobj <- hopach(eset.s,…

Clustering Clustering

updated 15.6 years ago • Rohit Farmer

div class="preformatted">Dear all, We have developed our own Affymetrix chip (Custom Express Array, PM- only with two species). I want to analyse the data with...m using the makeProbePackage available in the AnnotationDbi (for a R-2.13.0) but I got the following error message: Error in rep(NA, max(pm1, mm1, pm2, mm2)) : invalid 'times' argument I already tried an old version of R-2.9.1 with…

cdf limma AnnotationDbi cdf limma AnnotationDbi

updated 14.7 years ago • Helga Garcia

gt; To: bioconductor at r-project.org > Subject: F values from topTable with coef=NULL testing all zero or > all equal? > > Greetings > > This has probably been answered before, but I can't narrow the > search down enough...and documentation for eBayes and realized that the null > hypothesis for the F statistic is that all the expression val…

updated 14.2 years ago • Michael Muratet

div class="preformatted">Dear all, I get the following error when doing the Mas5 calculation using the Simpleaffy package: ============================================================ Rgui.exe has generated errors...and will be closed by Windows. You will need to restart the program. An error log is being created. ============================================================ More details: R…

Yeast affy simpleaffy Yeast affy simpleaffy

updated 21.7 years ago • Rudy.vanEijsden@GEN.unimaas.nl

Hey guys, I see an error in getting the working system see here [_isres1033-dll][1] to solve it. Find all updates to read these issues on the website

crlmm

updated 2.6 years ago • jenny

<div class="preformatted">I am attempting to use GRanges to calculate the distances between certain probes and their nearest respective transcription start sites. I have created two GRanges objects, one containing the position of the probes and another containing the positions of the genes (which I produced from USCS Table Browser). This is the code I used: genes<-GRanges(seqnam…

Transcription GenomicRanges Transcription GenomicRanges

updated 13.4 years ago • d r

div class="preformatted">Dear all, I encountered a problem while working on R that I do not know how to solve. It started when I wanted to load the affyPLM package...package: matchprobes Loading required package: splines Loading required package: preprocessCore Error in ls(where) : unused argument(s) (2) Error in library(affyPLM) : .First.lib failed for 'affyPLM'/* As packages such as 'affy'…

mouse4302 affyPLM mouse4302 affyPLM

updated 17.0 years ago • Wijchers, Patrick

Debian packages, and 779 directly installed from CRAN and BioConductor, covering over 99% of all packages at CRAN and BioConductor [ not counting a handful of windows-only CRAN packages] for complete coverage as of 25...via openoffice and koffice suites, abiword, gnumeric and other applications; - plus all the tools and toys from the current Knoppix relase. …

Coverage Visualization GUI Coverage Visualization GUI

updated 19.9 years ago • Dirk Eddelbuettel

RNAseq data from 2 different populations exposed to 2 experimental treatments. I get the following error when running edgeR: "error in dispCoxReid(y, design=design, offset=offset, subset=subset, : no data rows with required number...of counts." After this error is reported, R freezes and I must force quit the program. Im not using this function in my code so I am unsure why I am getting...the err…

edger rnaseq error

updated 11.3 years ago • melissabarrett747

div class="preformatted"> Dear users, I met an error when I tried to run expression data after normalization. The first two columns are probe_id and gene symbol, the rest...expression.csv") When I tried to use sampleNetwork() function to load the data, it generate an error: Error in SampleNetwork(datExprT = datE, method1 = "correlation", impute1 =FALSE, : expression matrix contains non-n…

updated 12.4 years ago • Guest User

Hi all,    Any help would be much appreciated. I have searched for this error and cannot find it anywhere but whats more weird...Time\_point + Organ) dds1 <- DESeq(dds, reduced = Organ, test = "LRT")... I am now getting this error: Error in DESeq(ddsAMIR, reduced = Organ, test = "LRT") :    object 'Organ' not found This is really confusing as the…

deseq2 LRT reduced model

updated 7.9 years ago • A

Hi, This type of error was already posted <https://support.bioconductor.org/p/37063/> but I don't see that it was resolved.   I've been...df <- getBM(attributes = c("ensembl_gene_id"),mart=mart) `` with no problems but now all of a sudden I'm getting this error: `` Error in getBM(attributes = c("ensembl_gene_id"), mart = mart) :  `` &nbsp…

biomaRt getBM

updated 8.8 years ago • rubi

is the most similar summary to VF for breakpoints that is available for breakends? I want to make a rule that determines whether a breakend is detected or not detected for each sample. I am considering using BANSR + BANRP &gt

StructuralVariantAnnotation

updated 6.2 years ago • Dario Strbenac

Dear Dr. Sanders,   I'm writing to inquire how to solve problems regarding HilbertVisGUI. I've installed gtkmm on my computer, but still have the following errors:   > library(HilbertVisGUI) Error in inDL(x, as.logical(local), as.logical(now), ...) :    unable to load shared object 'C:/Users/zhou23.TC/Documents/R/win-library/3.3/HilbertVisGUI/libs/…

R

updated 8.0 years ago • xz2256

for Cnetplot for rnrichResult obj given in the manual of enrichplot package but still getting this error. Can someone please help me with that? Code should be placed in three backticks as shown below ```r # include your problematic...B3B3B3", + size_item = 1, + color_edge = "grey", + size_edge = 0.5, + node_label = "all", + foldChange = NULL, + hilight_alpha = 0.3, + ) …

enrichplot clusterProfiler

updated 10 months ago • Ayesha

This error seems to be coming back and going away. It has been reported [before](https://stackoverflow.com/questions/61692990/topgo...giving-an-error-since-upgrade-to-v2-40-0). Code to reproduce it comes out of the vignette: ```r library(topGO) library(ALL) data(ALL) data(geneList...affyLib <- paste(annotation(ALL), "db", sep = ".") library(package = affyLib, character.only = TR…

GO.db topGO

updated 5.2 years ago • fklirono

I installed the package from zip (from the Bioconductor website), and also installed all the packages it asked for. It went all succesfull: "package 'IlluminaHumanMethylation27k.db' successfully unpacked and...MD5 sums checked" But when I am trying to load this library I get an error: > library(IlluminaHumanMethylation27k.db) Loading required package: AnnotationDbi Loading required pack…

updated 15.4 years ago • Kristel van Eijk

Hello all, I am working on Trinity for denovo assembly of my data but stuck at differential gene expression step(screenshot). I have...3 sample files and followed the steps as mentioned in the trinity tutorial but somehow getting this error in edgeR. ``` Error, cmd: R --vanilla -q < matrix.counts.matrix.align_estimate_rsem_P3_vs_align_estimate_rsem_unP3.align_estimate_rsem_unP3.vs.al…

edger

updated 6.7 years ago • sakshi.rajput55

model.matrix(~0+f) >  colnames(design) <- lev >  fit <- lmFit( eset, design) Error in as.vector(x, mode) :  cannot coerce type 'closure' to vector of type 'any' this is the message i am getting, when i try to...work with around 117 cel files. Target file and design seems to ok. but still i am getting error message. Please some one help regar…

updated 16.9 years ago • Ayyarappan Bharathi

hello, i am not an expert in R and i am trying to use MEDIPS package for medip-seq data analysis. But i am having this error er=MEDIPS.CpGenrich(file=bam.file.hESCs.Rep1.MeDIP, BSgenome="BSgenome.Hsapiens.UCSC.hg19", chr.select="chr22", extend=0, shift=0, uniq=1e-3) Reading bam alignment hESCs.MeDIP.Rep1.chr22.bam Selecting chr22 Total number of imported short reads: 152586 Creati…

software error Grange RangedData

updated 5.9 years ago • mawusse.agbessi

getting message: cannot open compressed file 'C:/PROGRA~1/R/R-22~1.0DE/library/affy/R/all.rda' Error in library(affy) : .First.lib failed for 'affy' (run on windowsxp prof. R 2.2.0 dev and all packages are dev) Running simpleaffy...x.rma, "animal", c("1", "2"), raw.data) Getting probe level data... Computing p-values Error in as.double(pms[, x]) : subscript out of bounds Thanks for help. Nare…

probe affy simpleaffy probe affy simpleaffy

updated 20.4 years ago • Narendra Kaushik

Hi All, When I try to download GSE49656 with GEOquery, errors were always reported: such as __not all columns named in 'colClasses...Hi All, When I try to download GSE49656 with GEOquery, errors were always reported: such as __not all columns named in 'colClasses' exist__   When I change to server (linux), some other error reported: __Error in read.table(con, sep = "\\t", header = F…

GEOquery

updated 9.1 years ago • Shicheng Guo

meta-data package as described in "How to use Resourcerer". Everything goes fine (except the kegg errors) until this error: library(Resourcerer) resourcerer2BioC("Agilent_Human1Av2.zip", organism="human", destDir=file.path...path.package("Resourcerer"), "temp"), pkgName=("AgilentHuman1Av2"), srcUrls=getSrcUrl("all","Homo sapiens"), pkgPath=file.path(.path.package("Resourcerer"),"temp"), otherSrc…

convert Resourcerer convert Resourcerer

updated 20.6 years ago • Morten

<div class="preformatted"> Dear list, I get an error when I try to import an xls file obtained from the SMD database using the read.SMD function of the marray package. The error occurs only if the file is not placed in the working directory. More in detail, if the file 'myfile.xls' is placed on the 'path/to/dir' directory and the command: read.SMD(fnames = "myfile.xls", path = "path/to/…

marray marray

updated 14.2 years ago • Guest User

by MACS, so the output peaks file is empty. When I use that file in DiffBind sample sheet, I get an error: <pre> Error in read.table(fn, blank.lines.skip = T, header = T) : no lines available in input Calls: dba ... pv.peakset -> pv.readPeaks...gt; pv.macs -> read.table</pre> Is there a way to suppress that error? <span style="line-height:1.6">I understand…

diffbind chipseq

updated 9.5 years ago • igor

I'm trying to download ChAMP package. When doing so I'm getting the following error Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.1.0/library packages: Matrix...mgcv Old packages: 'Rcpp' Update all/some/none? [a/s/n]: Does anyone know how to solve this

ChAMP

updated 4.5 years ago • FWNL15

div class="preformatted">I am getting a package cannot be found in any repository error for all packages, but I am able to get getBioC.R. Is there something up with the repository? Newly installed R 1.9.1, MacOS

updated 21.4 years ago • Sean Davis

Hi all, I am attempting to run the dexseqcount.py script using alignedreads.sam and flattened_file.gff as input files. Unfortunately...Hi all, I am attempting to run the dexseqcount.py script using alignedreads.sam and flattened_file.gff as input files. Unfortunately, I have been receiving the error "line 120 raise SystemError, "illegal strand". I wanted to ask how to correct this …

software error

updated 5.6 years ago • huck.thornton

filters ="ensembl_gene_id",values="ENSG00000206557",mart=hmart) > show(gene.map) As long as all Human genes are uniquely identified through their respective "hgnc_symbol" I am fine. Why should I use the other identifier...entering "Human" species and miRNA identifier "hsa-miR-yyy" TarBase interface returns a list of all gene ENSGxxxxxx that have been experimentally tested. I input such …

miRNA miRNA

updated 16.5 years ago • mauede@alice.it

I got error while installing esATAC on Ubuntu 16.04 LTS. devtools::install_github("wzthu/esATAC") fastq_io.h:30:10: fatal error: zlib.h...compilation terminated. make[1]: *** [Makefile:46: demultiplex.o] Error 1 make[1]: Leaving directory '/tmp/RtmpOcp5qQ/R.INSTALLd5ad4c460074/Rbowtie2/src/adapterremoval' make: *** [Makefile:10...all] Error 2 ERROR: compilation fa…

software error esATAC zlib.h Ubuntu Tutorial

updated 6.5 years ago • vedbar

div class="preformatted">Dear Jakob, I've never seen this error, despite using duplicateCorrelation() often. Please provide a reproducible example so that the error can be tracked...0200 > From: "Jakob Hedegaard" <jakob.hedegaard agrsci.dk="" at=""> > Subject: [BioC] Limma - error when using duplicateCorrelation > To: <bioconductor at="" stat.math.ethz.ch="">…

Genetics limma Genetics limma

updated 19.3 years ago • Gordon Smyth

<div class="preformatted">Dear All, Since the hgu133atagprobe package is not available from the bioconductor website, I am trying to construct it by using makeProbePackage. But this function return the following error: "Expected but did not find the log-file hgu133atagprobe.Rcheck/00check.log after R CMD check" (bug??) So I let the check = FALSE...div class="preformatted">Dear All, …

updated 21.0 years ago • Yingtao Bi

I am resolving the warning about the packages, and then when I try again to run the app all the time I am getting Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org

BiocInstaller BiocManager Bioconductor

updated 5.0 years ago • adklts

Dear all, I am using DESeq2 to estimate fold changes of treatment versus control in a time series experiment (with biological replicates...about the standard deviations of the fold changes provided by DESeq2. These are almost constant over all timepoints, although it doesn't look like this when I judge the biological replicates in the output of plotCounts...Can someone please enligh…

deseq2 log2fc standard error timecourse

updated 7.9 years ago • Verena

div class="preformatted">Dear all I am trying to read a GSE file in R using GEOquery package but i am getting following error.Kindly tell me why i am getting...this error. I have tried to find out on google. But no luck... u <- getGEO(filename="GSE1106_family.soft",GSEMatrix=TRUE) Parsing.... Found...22 entities... GPL199 (1 of 22 entities) GSM18235 (2 of 22 entities) GSM18236 (3 of 2…

GEOquery GEOquery

updated 11.1 years ago • Reema Singh

Hi all, I am trying to compile the updated genome of the model plant Arabidopsis thaliana, from TAIR10. I am using the function...Hi all, I am trying to compile the updated genome of the model plant Arabidopsis thaliana, from TAIR10. I am using the function forgeBSgenomeDataPkgFromNCBI but I am running to the error that the data contains ambiguity characters in sequences. I used Biostrin…

BSgenomeForge

updated 2.4 years ago • Bruno

format (instead of .sf format?). I have followed the Users manual of DESeq2 to tximport but got the error at txi step. > files1 <- list.files( pattern = ".txt",full.names = TRUE) > names(files1) <- paste0("samples", 1:4) > all(file.exists...files with read_tsv 1 2 3 4 summarizing abundance summarizing counts summarizing length Error in…

deseq2 tximport

updated 7.0 years ago • saddamhusain77

Hi All, 1.   I'm trying to use the code below to shrink the LFCs in my model but I keep generating an error. <pre> resLFCint <- lfcShrink...dds, res = res, name="Cov1.Conditioncase", type="apeglm")) using 'apeglm' for LFC shrinkage Error: !missing(coef) is not TRUE design ~ Age + Gender + Cov3 + Cov2 + Cov1 + Condition + Cov1:Condition </pre> where C…

deseq2 interaction term

updated 7.4 years ago • Cece

Dear all,   When I load a library, this keeps coming out: __library("AnnotationDbi") Loading required package: IRanges Error in unloadNamespace...Dear all,   When I load a library, this keeps coming out: __library("AnnotationDbi") Loading required package: IRanges Error in unloadNamespace(package) :    namespace ‘IRanges’ is imported by ‘An…

software error

updated 9.9 years ago • xlyan011

Hi all, I have a fairly complex ChIP-seq experiment with lots of treated/untreated groups, 2 replicates each. All the 'replicate...Hi all, I have a fairly complex ChIP-seq experiment with lots of treated/untreated groups, 2 replicates each. All the 'replicate 1s' were generated together, separately to the 'replicate 2s' and I can see that that effect is quite pronounced in the final matrices, t…

diffbind batch effect

updated 9.4 years ago • Jon Manning

model fits very poorly, like the two examples you give. I've just run an overall test (between all the time points) on your data, and I find most of the transcripts in the your data set to be differentially expressed, at high...the algorithm would fail to converge when > trying to fit to them? I'm thinking if there were a rule I could apply I > could probably just drop them and sav…

GO GLAD edgeR GO GLAD edgeR

updated 14.9 years ago • Gordon Smyth

div class="preformatted">Hi I am trying to use matchPDict() and below's the error I get. This happens with my objects as well, but I am showing the vignette example. thanks in advance -burak # I've made sure...strand + of ce2 chromosomes chrI, chrII, chrIII, chrIV, chrV, chrX, chrM >>> Finding all hits in strand + of chromosome chrI ... Error in initialize(value, ...) : …

BSgenome BSgenome BSgenome BSgenome

updated 16.9 years ago • burak kutlu

Expressionists, In running maDiagnPlots1 on the swirl test dataset, received the following error message: > maDiagnPlots1(swirl[,2], title="Swirl array 93: Diagnostic Plots", + save=TRUE, fname="swirl93.jpeg", dev="jpeg") Error...plot.new() : Figure margins too large I am running R1.8.0 Windows XP and marrayPlots 1.1.6 All of the previous marraPlots functions wo…

Cancer Cancer

updated 22.2 years ago • Richard Friedman

form of ImaGene TXT format. As described in the package, I make a folder named Exiqon and paste all relevant data there, set working directory on R and start working. But when I want to read all my files it shows error - &nbsp...Error in file (file, "rt") : cannot open the connection. I check my current working directory, set all files clearly there...ebatch &lt…

R eximir microrna

updated 9.8 years ago • 31sharmajittu1991

<div class="preformatted"> Hello, I am trying to do GO enrichment analysis. When I use ???GOFrame???, I get the following error message: > frame = toTable(org.Rn.egGO) > goframeData = data.frame(frame$go_id, frame$Evidence, frame$gene_id) > goFrame = GOFrame(goframeData, organism = "Rattus norvegicus") Error in .testGOFrame(x, organism) : All of the Evidence codes in …

GO Organism rat2302 AnnotationDbi GO Organism rat2302 AnnotationDbi

updated 12.8 years ago • Guest User

matchGenes of the package bumphunter to associate many regions of interest with transcripts. I use all=TRUE in order to get several results per region. When I use all=TRUE and a small amount of queries, the output indeed contains...columns 'queries' and 'Tx' which give the query index and the matching transcript. But when I use all=TRUE and many regions (when the function starts to split the dat…

Annotation bumphunter Annotation bumphunter

updated 12.5 years ago • Anne Biton

at unavarra.es >To: bioconductor at r-project.org >Subject: [BioC] Diffbind error >Message-ID: > <e6a0d8855033e937b5236f5787e1d78d.squirrel at="" webmail.unavarra.es=""> >Content-Type: text/plain...gt; >Chip_K27.2+ Neural K27 Responsive 1 Chip_K27d.BED Input_K.BED >Chip_K27d.BED > >--All my BED files have 6 lines and have …

DiffBind DiffBind

updated 13.1 years ago • Gord Brown

Hi all, I have just used the makeOrgPackagefromNCBI() to create a db for Verticillium dahliae using the following code: I think...using clusterProfiler and AnnotationDb, but when I try to install the `("org.Vdahliae.eg.db")` this error appears: Please, do you have any suggestion on how to solve this error? I have already tried to update BiocManager (v3.18

AnnotationForge

updated 20 months ago • Patadù

txt and row data (gpr). Now i want used bioconductor to generate a nomalized intensity matrix for all knockout experiments. I thought i have to use limma package and tried to read the data with marray function read.GenePix...but there is still an error. Then I tried to read the info txt but there is still an error too. Maybe i just chose the wrong package for my dataset. Unfortunately...help --…

limma marray ArrayExpress limma marray ArrayExpress

updated 13.9 years ago • Guest User

div class="preformatted">Hi all, How do I fix the following error?? INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord SCANN THE DATA USING AFE 9.5.3.1 Error

updated 13.7 years ago • matthew vitalone

div class="preformatted">Dear All, I am working with 13 different data sets (containing 550 arrays in total) which is normalized using general linear model...for print-tip. I am trying to do following: 1) Merging all 13 different data sets: To merge these data sets I built ExpressionSet for each data set. Then I made a list of these ExpressionSets...new("RGList", list(R=red, G=green)) norm1 …

arrayQualityMetrics arrayQualityMetrics

updated 16.3 years ago • Amit Kumar

I am analyzing two MACS2 bed files using ChIPseeker. Individual analysis is OK, but I'm getting an error message for simultaneous analysis of two files when using following ChIPSeeker functions: plotAnnoBar, plotDistToTSS...and vennplot. All error messages are similar:<span style="background-color:Yellow"> </span>_<span style="background-color:Yellow">Error in XXXX...peakAnnoLis…

ChIPseeker named list error plotAnnoBar plotDistToTSS vennplot

updated 7.9 years ago • k.panov