Bioconductor Forum

div class="preformatted">Hi, I keep getting an error message when i try to generate the dataset file in RNAither. This is the error i keep getting. > generateDatasetFile...8, 12, 1, emptyWells, poorWells, controlCoordsOutput, backgroundValOutput, cellnumOutput) Error: could not find function "generateDatasetFile" Can anyone help explain why this is happening? At the beginning, as usu…

updated 13.9 years ago • Catherine Garry

no seqlengths</pre> We import the scores from BigWigFile like this: <pre> gr_frq_mtx = import.bw(snakemake@input[['g1000SNPTrack']], which = motifs_gr,                            as = 'NumericList

R rtracklayer data import

updated 7.5 years ago • stefan.dvoretskii

am trying to read and normalize an Agilent dataset but i have this error : Error in file(file, "r") : cannot open the connection, and aslo when i tried this code to check the files : targets$FileName\[!file.exists...FileName)\]   its works with out problem   I used targets$FileName the out put all the file name  with information in targets file ? no prob…

limma

updated 10.7 years ago • naving2uk

with RGui.exe there is no problem, but if I try to execute through a BAT file (windows 10) I have an error: bat file: "C:\Program Files\R\R-3.5.2\bin\Rscript.exe" "C:\r\filo.R" error: ERROR: Cannot open output file [internalRsequence.aln...Error in convertAlnRows(result$msa, type) : There is an invalid file! Calls: msa->msaFun->convertAlnRows Ejecución interrumpida...It se…

software error

updated 6.8 years ago • albizu.m

data set using the lumiR() function, the data are Illumina Bead Studio output. I get the following error message: "Error in var(x, na.rm = na.rm) : 'x' is empty" I am new to R and am not familiar with all the functions, is it possible there

updated 18.3 years ago • jarod07@ucla.edu

div class="preformatted">On Fri, May 20, 2005 2:29 am, M Perez said: > Thanks Gordon for all your answers. > > I am afraid I have more questions, now about "normexp" > background correction, I am trying to use "normexp...gt; with Limma 1.8 and I got this error > >> RG <- backgroundCorrect(RG, method="normexp", > offset=100);…

limma limma

updated 20.7 years ago • Gordon Smyth

Hello, I am having a problem performing vst normalisation on my data. I get the following error message that I can't make head or tail of: > lumi.T <- lumiT(lumi.B) Perform vst transformation ... 2011-02-25 11:07:29 , processing...array 1 Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 0 (non-NA) cases I have searched the archives and found that peopl…

lumi lumi

updated 14.9 years ago • Sarah Allen

<h3 style="direction: rtl;">Hi all,</h3> During I working for DNA microarray data analysis using Bioconductor , I faced some problem about Quality Control &nbsp...h3 style="direction: rtl;">Hi all,</h3> During I working for DNA microarray data analysis using Bioconductor , I faced some problem about Quality Control...When I have written this command qc() for example qc(…

qc

updated 10.2 years ago • libya.tahani

div class="preformatted">dear all, I am using lumi to normalize raw Illumina Data, but when I run the script, I retrive this error. can you help me? library(lumi

probe lumi probe lumi

updated 17.2 years ago • John Lande

div class="preformatted">Dear Members, I am trying to download the 3'UTR sequences of all human genes from Ensembl Biomart using the package biomaRt. Ideally, after retrieving I want to save these in FASTA format...in chromosome 1, 2 and 3 (not sure if this is the best way to achieve what I want), I am getting an error: "Error in getBM(attributes = c("hgnc_symbol", "3utr"), filters = "chrom…

biomaRt biomaRt

updated 13.5 years ago • Karthik K N

nbsp; I'm having an error with the importing of Salmon data via tximport. <pre> txi.all <- tximport(all_files, type = "salmon", tx2gene = tx2gene) reading...missing from tx2gene: 36704 summarizing abundance summarizing counts summarizing length Error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE In addition: Warning messages: 1: In rowsum.default(abundan…

tximport salmon R bioconductor

updated 8.5 years ago • macmanes

<div class="preformatted">Hello group, I am trying to read my cel files using read.affybatch method. I stored all my cel files, probe information file and experiment file in one directory. I used the following commands: >fls = list.files() >ab = read.affybatch(filenames=fls) Error in initialize(value, ...) : Is breastCancerData_2.txt really a CEL file? tried reading as tex…

probe affy probe affy

updated 21.6 years ago • S Peri

and everything runs smoothly except one thing -> I cant make a dba.report for one of my contrasts. All steps from loading -> counting -> analyzing seems to work, I get differently called peaks etc. I have 4 different conditions...2 952</pre>   What really puzzles me is that I have done the exact same workflow for all my samples, but it's just one single…

diffbind

updated 8.7 years ago • j.bergenstrahle

Hi , I'm having an error in exomeCopy when I computate fit. (No previous error, following the vignette, and with provided data). > fit <- exomeCopy...Hi , I'm having an error in exomeCopy when I computate fit. (No previous error, following the vignette, and with provided data). > fit <- exomeCopy(counts\[seqnames(counts) == + "chr1"\], sample.name = "BIR", X.nam…

exomecopy

updated 7.9 years ago • chiara.rigobello

Hi, I am trying to download devel version of minfi , I got an error due to dependency error of bump hunter library Any idea? \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\# <pre> biocLite("minfi") BioC_mirror: https://bioconductor.org Using...Installing package(s) 'minfi' also installing the dependency 'bumphunter' downloaded 0 bytes Error in download.file(url, destfile, method, mode = "wb",…

bumphunter

updated 9.5 years ago • Asma rabe

When using the coMET package in R, I always meet the error as the following: Error in unit(at, "native") : 'x' and 'units' must have length > 0 In addition: Warning messages: 1: In min(at) : no non...returning Inf 2: In max(at) : no non-missing arguments to max; returning -Inf But I prepared all the file according to the coMET user guide, I couldn't understand what this error mean…

software error annotation

updated 5.6 years ago • yueli.yao

Hi all, I'm trying to create a dendrogram with qualitative data in a txt file. This is what I have so far: > RQ1_cloud <- readLines...dist(t(dtmss), method="euclidian") > fit <- hclust(d, method="complete", members= NULL) Error in hclust(d, method = "complete", members = NULL) : NA/NaN/Inf in foreign function call (arg 10) However, I get an error with that sa…

dendrogram hclust textanalysis R RStudio

updated 4.7 years ago • Abby

that contrast does not apprear in the ```resultsNames(dds)```, so the ```lfcShrink()``` gives me an error. Thanks for any help in advance! ``` dds <- DESeqDataSetFromMatrix( countData = countdata, colData = coldata, design = ~ replicado...comp_down, log2FoldChange) #write.csv(comp_down, paste0(a,"vs",b,"_down.csv")) return(list("ALL"=comp , "UP"= comp_up, "DOWN"=comp_down…

DESeq2 resultsNames lfcShrink

updated 3.4 years ago • eve.olszanowski

<span style="line-height:1.6">I am getting an error message trying to run fitTimeSeries from metagenomeSeq:</span>     <span style="line-height:1.6">fitTimeSeries(obj, feature=1, class="Class", time="Time" , id="Sample")</span> Error in Summary.factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  :    min not meaningful for…

metagenomeSeq microbiome

updated 11.0 years ago • noelle.noyes

div class="preformatted"> Dear all, Having an error message come up when trying to use qc on my bovine affy genechips "Error in setQCEnvironment(cdfn) : Could...for the alphas and controls? Any help would be apprecaited. I am new to this and still figuring it all out. Thanks Louisa Rispoli "If we knew what we were doing, it wouldn't be called Research." - Albert Einstein </div

cdf cdf

updated 18.3 years ago • Louisa A Rispoli/AS/EXP/UTIA

Hi all, Would you suggest how to fix this error? I have only 2 replicates for the control and 2 replicates for the diseased group...default model design and contrast(s)... Analyzing... Adding contrasts(s)... Analyze error: Error in pv.DBA(DBA, method, bTagwise = bTagwise, minMembers = 3, bParallel = bParallel): Unable to perform analysis: no contrasts

ATACSeq

updated 2.8 years ago • Chris

Hi everyone I need to run Deseq2, but when I try to run this part of command the following error message appears. **Error in DESeqDataSet(se, design = design, ignoreRank) : design has a single variable, with all samples having...renamed by adding numbers** I am new to R and DESeq2, Please anyone could hepl me to fix this error. Thank you very much

DESeq2

updated 4.3 years ago • Abdou-samad

div class="preformatted">Dear All, I am trying to analyze a Microarray series data using "GEOquery". I get the below error when trying to extract the information...gt; gse = getGEO("GSE15709"); > Meta(gse) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "Meta", for signature "list" > GSMList...gse)[[1]] Error in function (classes, f…

Microarray Microarray

updated 16.4 years ago • Kishor Tappita

<div class="preformatted"> dear all, I was trying to apply dmrFinder function in bsseq package, but it always gives the following error: ################################################## dmrs0 <- dmrFinder(BS.cancer.ex.tstat, cutoff = c(-4.6, 4.6)) segmenting splitting creating dmr data.frame Error in ifelse(regions$meanDiff > 0, "hyper", "hypo") : error in evaluating the…

bsseq bsseq

updated 12.2 years ago • Guest User

<div class="preformatted">Hi All I am trying to cluster 57 COGs in 24 datasets. I use the following code and run into this error: hc = NULL hc <- hclust(as.dist(1-cor(as.matrix(bb), method="spearman")), method="complete", members=NULL) Error in hclust(as.dist(1 - cor(as.matrix(bb), method = "spearman")), : NA/NaN/Inf in foreign function call (arg 11) In addition: Warning message…

updated 13.6 years ago • Alyaa Mahmoud

div class="preformatted">Dear all, first of all I apologise if this is a silly question. I am using R version 1.7.1 Beta I am trying to create objects of class...2 6 sample6.txt control treated 2 and then tried to load it... and got the following error: > mydata.samples<- read.marrayInfo(file.path(datadir, "samples.txt")) Error in paste.default("Invalid object for

updated 22.5 years ago • kfbargad@lg.ehu.es

sWGS data. Initial results showed CNAs in centromeres areas of several chromosomes, recurrently in all samples (benign and tumor samples). I am trying to mask centromeres and telomeres, following the instructions: ```r bins$blacklist...Downloads/wgEncodeDukeMapabilityRegionsExcludable.bed")) ##The error is the same; ##...Error in as.vector(data) : ##no method for coercing this S4 class to …

QDNAseq blacklist CopyNumberVariation blocklist

updated 4.1 years ago • briverog

If the biological interest is to see each inhibitor effect separately, does it make sense to include all the chips together for the analysis, or only one inhibitor at a time? In addition, what if the inhibitor only experiments...B effect is little. My question is whether the linear model still hold (since B is now included in error variance?). Xiwei -----Original Message----- From: Fangxin Hon…

limma limma

updated 21.0 years ago • Wu, Xiwei

Dear all, I am not very familiar with R and get error massages like this: **"Batch submitting query [==================================>------------------] 67% eta: 3sError in getBM(filters...length 1. Please report this on the support site at http://support.bioconductor.org"** They are all the same but differ in progress [%] and time [s]. A few days before everything was wor…

biomaRt ensembl

updated 5.8 years ago • nina.hahn

Hi all, I am using uniport.ws library for retrieving uniport web services of Human dataset. But when i run the function up = UniProt.ws...taxId = 9606) then it gives this error <pre> Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") : cannot open URL 'http://www.UniProt.org

bioconductor uniprot.ws

updated 10.1 years ago • beingseema03

Hi, When forging a BSgenome I'm getting this error : ``` > "Error in .readSeedFile(x, verbose = verbose) : seed file > 'SARSCOV2-seed' must have exactly 1 record" ``` This is the code I'm running...Hi, When forging a BSgenome I'm getting this error : ``` > "Error in .readSeedFile(x, verbose = verbose) : seed file > 'SARSCOV2-seed' must have exactly …

BSgenome

updated 5.7 years ago • Didi

Hi all, Please let me know how I should go about in fixing this error. <pre> > pData(bg) ids treatment genotype 1 B1C_01 control resistant...Hi all, Please let me know how I should go about in fixing this error. <pre> > pData(bg) ids treatment genotype 1 B1C_01 control resistant 2 B1T_01 inoculated resistant > prr01_trans_result=sta…

R rnaseq Ballgown

updated 8.0 years ago • amy16

CAGE data and are trying to apply the cagefightR package. Unfortunately we got the following error message: "Error in asMethod(object) : all the ranges in the object to coerce to GPos must have a width of 1" Can someone help...us understanding where is our error, and how to correct it ? Here is the code: library(CAGEfightR) library(stringr) bw_path <- "../elaborated_data/dire…

CAGEFightR CAGE CTSS

updated 6.7 years ago • July

<div class="preformatted">Dear all, I am a new user of Bioconductor. I was trying to use the function "featureFilter" from genefilter package and got the following error message. nnon_ed<-featureFilter(ed,require.entrez=TRUE,require.GOBP=TRUE,remove .dupEntrez=TRUE,feature.exclude="^AFFX") Error in rowQ(exprs(imat), which) : which is larger than the number of rows For the same …

genefilter genefilter

updated 16.7 years ago • ywchen@jimmy.harvard.edu

GEOquery. It worked fine for most of the datasets except for a couple of them, I get the following error: * * Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input * * This is the script line I...these directly; GSE37830 = getGEO (filename = "GSE37830_family.soft.gz") but I still get the same error. Please advise Thanks a lot Alyaa Mahmoud…

GEOquery GEOquery

updated 13.0 years ago • Alyaa Mahmoud

Hi, all! I'm in trouble with installing "HPO.db" R package on linux as below.  <pre> > install.packages("HPO.db_1.7.tar.gz") inferring...installing help indices ** building package indices ** testing if installed package can be loaded Error in sqliteSendQuery(con, statement, bind.data) : error in statement: disk I/O error Error in sqliteSendQuery(con, statement..…

R

updated 9.7 years ago • brlee0920

bam files using qQCreport module of QuasR. My files are aligned, sorted and indexed. It shows error: Error in .normarg_totalsize(totalsize) : 'totalsize' must be a single integer My code is pasted below: ``` > library(QuasR) &gt...gt; proj1 <- qAlign(sampleFile, genomeFile, paired="no") Creating .fai file for: D:/genome.fa all necessary alignment files found …

QuasR qQCReport QuasR error Error in .normarg_totalsize(totalsize)

updated 6.0 years ago • A.Singh

div class="preformatted">Hi all, I'm new to this list, so let me introduce myself very shortly. I'm working at the Laboratory of Microbial Ecology and Technology...I like the idea to standardize the way of data storage and handling. So, are there already any 'rules' or 'guidelines' about such standardization for data storage etc.? I just want 'my package' be compatible with other stuff

updated 22.4 years ago • Kurt Sys

gff1) ``` The same using `import.gff3` and `makeTxDbFromGFF()` or any combination. This is the error (with traceback): ```R Error in as.vector(x, mode) : coercing an AtomicList object to an atomic vector is supported only for objects...from this, the instructions for importing the GFF in the help docs (see below) exits with another error at `import()`: Code in the docs ```R library(rtr…

genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges

updated 6.8 years ago • xvazquezc

dens<-csDensity(genes(cuff)) dens # This works fine and displays a density plot. But, if I run all this again on a different set of samples, I get this. library(cummeRbund) setwd("C:/Users/mark/Documents/Cross/cufflinks_data...diff_colon_1_3_0/d iff_colon_1_3_0") cuff<-readCufflinks() dens<-csDensity(genes(cuff)) dens Error: attempt to apply non-function Any ideas how I c…

cummeRbund cummeRbund

updated 14.0 years ago • john herbert

from and documentation for eBayes and realized that the null hypothesis for the F statistic is that all the expression values are zero. I want to test the hypothesis that all the expression values are equal, i.e., rejection implies...it with coef=NULL will yield an F statistic calculation, and I infer from the docs it will include all the conditions. What is the null hypothesis: that all the valu…

updated 14.2 years ago • Michael Muratet

Hi all- I'm currently trying to annotate Ensembl ID of my RNAseq output with gene names with biomaRt and I use the function getBM...Hi all- I'm currently trying to annotate Ensembl ID of my RNAseq output with gene names with biomaRt and I use the function getBM. However, it keeps giving me the error: "no such table: metadata". I guess it's not something wrong with my input since I have the sam…

biomaRt software error

updated 5.6 years ago • JINYI

<div class="preformatted">Dear all, I want to analyse my affy data with limma. I have 3 genotypes A, B, C I want to compare to the reference ref, and 3 replicates for each genotype and ref, so 12 arrays. I have this error message I don t understand: > data<-ReadAffy() > eset<-rma(data) > design ref A B C Exp143hyb246 1 0 0 0 Exp143hyb…

affy limma affy limma

updated 22.4 years ago • Delphine Fleury

pms <- pm(data) > pm.i <- indexProbes(data,which="pm") which seems to have given me the all the data I need, but when I try and add them to a data frame or use write.table, I get an error: > data.frame(names,pms,pm.i) Error...287306, : arguments imply differing number of rows: 16, 11, 8, 9, 10, 20, 69 The same error, when trying to write the indices by them…

probe probe

updated 21.4 years ago • Thomas Turner

<div class="preformatted"> Hi all, I am trying to load my agilent data to Limma using read.maimages function. Here's what I did: > library(limma)> targets&lt...div class="preformatted"> Hi all, I am trying to load my agilent data to Limma using read.maimages function. Here's what I did: > library(limma)> targets...annotation = c("Row", "Col","FeatureNum"…

limma limma

updated 14.2 years ago • Ella Chang

Hi all, I am facing an error using on the package “__VariantAnnotation__” It is one of the dependencies for my package hosted on...GitHub and currently a lot of the users with latest R version are facing this error. ‘invalid class "VRanges" object: 'strand' should be a 'factor' Rle with levels c("+", "-", "\*")’ The package works fine with the R version 3.3.2...but fails with the above mentio…

variantannotation VRanges R Rle

updated 7.6 years ago • Jayendra Shinde

Hi, I got this error  \`make: \*\*\* \[ShortRead.so\] Error 1\`  while installing ShortRead in the following way: <pre> > source("http://bioconductor.org...could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [ShortRead.so] Error 1 ERROR: compilation failed for package ‘ShortRead’ * removing ‘/home/waterhouse/R/x86_64-pc-linux-gnu-l…

shortread

updated 9.6 years ago • mictadlo

increasing flood of microarray and NGS, “Big Data” (e.g., TCGA Data), especially in the form of rules, understandable by human experts and by machines, too. We are now involved in studies discovering rules, for understanding

cancer microarray mirna sequencing

updated 10.8 years ago • alexandru.floares

Dear All, Using R and BioMart, I get the following error message when trying to access the coding sequence of a gene: ``` mart <- useMart...seqType = "coding", mart = mart) ``` NULL Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery, : The query to the BioMart webservice returned

software error biomart error28

updated 5.8 years ago • heiko_kin

    Dear All,  I am receiving the following error after installing ArrayQualityMetrics <pre> onLoad failed in loadNamespace() for 'Cairo', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Users/rkrams/Library/R/3.4/library/Cairo/libs/Cairo.so': dlopen(/Users/rkrams/Library/R/3.4...nbsp;   Dear All,&…

software error

updated 8.4 years ago • robertkrams

<div class="preformatted">Hi, We've looked into the problem - it arises because the raw annotation data used to build the annotation files in the "hgu133a" package ommited some probesets in the latest build. This was breaking the annotation lookup calls in simpleaffy. (The issue was occuring within the results.summary() function).I've added a work around to the package to deal with this (…

Annotation Cancer hgu133a probe simpleaffy Annotation Cancer hgu133a probe simpleaffy

updated 20.5 years ago • Crispin Miller

Hi, I found following error when I tried running the following example code from regioneR vignette.  <pre> pt_Rad21_5k_vs_Ctcf <- permTest...count.once=TRUE, + genome="hg19", mc.set.seed=FALSE, mc.cores=4) Error in if (alt == "less") { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In mclapply(c(1:ntimes), r…

regioner overlappingpeaks

updated 8.7 years ago • tharveshliyakat

div class="preformatted">Hi all, I met an error when I use splicing.index with by.chip=T. > si.em_nv_bychip <- splicing.index(x=x.rma, genes=sig.genes...group="cell_type", members=c("EM", "NV"), by.chip=T) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "rowttests", for signature "matrix", "character

updated 17.7 years ago • Xin Zheng

<div class="preformatted">Dear list, --I'm trying to use Diffbind package to analyze some samples from a ChIP seq experiment. --I created a .csv samplesheet with the following fields and which samples to analyze: SampleID Tissue Factor Condition Replicate Reads Control Peaks Chip_K27.1+ Neural K27 Responsive 1 Chip_K27.BED Input_K.BED Chip_K27.BED Chip_K27.2+ Neural K27 Responsiv…

DiffBind DiffBind

updated 13.1 years ago • José Luis Lavín

class="preformatted">Hello, I've just tried to install the GOstats package, and I get the following error: > library(GOstats) Loading required package: graph Creating a new generic function for "print" in "Ruuid" Loading required...openVignette() For details on reading vignettes, see the openVignette help page. Error in f(libname, pkgname) : couldn't find function "a…

GOstats GOstats

updated 21.6 years ago • Arne.Muller@aventis.com

div class="preformatted">Hi, I am getting errors from annaffy when I try to use it on "mgu74av2", depending on what columns I request/exclude or call the function a second...time: > anncols <- aaf.handler() #all! > andiff <- aafTableAnn(probeTop, "mgu74av2", anncols ) Error in `parent.env<-`(`*tmp*`, value = NULL) : use of NULL environment is de…

GO Survival mgu74av2 cdf annotate affy limma gcrma matchprobes annaffy simpleaffy plier

updated 19.0 years ago • Ido M. Tamir

div class="preformatted"> Dear all, I???m trying to use DESeq2 but I get this error message when I try the code: res <- results(dds) Error in is.numeric(cooksCutoff...cooksCutoff' is missing I can't find any answer about this error. Could you please help me? Thanks in advance! Cheers Natalia -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013

DESeq2 DESeq2

updated 12.1 years ago • Guest User

Hi, I am getting this error below and Summary and Off-targets file are not created. I would appreciate any suggestion. Thanks, Dawid Building feature...vectors for scoring ... Calculating scores ... Error in `$<-.data.frame`(`*tmp*`, "score", value = c(0.0112619406241216, : replacement has 443126 rows, data has 443130 **This the code below...BSgenomeName…

crisprseek

updated 6.9 years ago • Dawid G. Nowak

div class="preformatted">Hi, all, When I ran my old chip data (RN U34 chips) with gcrma, I got the following error. I had no problem with other chip types. Can someone

gcrma gcrma

updated 20.7 years ago • Puhong Gao

rma function. I have to read more than 100 files of 10MB each as a group and use rma function over all of these . I am trying to read those but it is giving me memory allocation probem. I have increased the memory using the memory.limit...size=) however it is still giving error that it cannot allocate vector. Please guide me on what I can do to avoid this problem. Regards, Tapan Mehta</div

Microarray Microarray

updated 22.7 years ago • Tapan Mehta