Bioconductor Forum

hi all I've been trying to run CopywriteR, which requires S4Vectors to run. after it creates the bam and bed files, it throws the...error below: <pre> lement index: 1, 2, 3, 4, 5, 6, ... first error: could not find function "subjectHits"</pre> I thought it was because I didn't have...and how I can get around this..and it's frustrating because CopywriteR runs for like 7hrs on…

s4vectors copywriter

updated 7.8 years ago • TriS

orgdb library using the package AnnotationForge, and when i enrich the GO annotation there is an error as bellow: **Error in testForValidKeytype(x, keytype) : Invalid keytype: GOALL. Please use the keytypes method to see a listing...GID", OrgDb = org.Aaltissimus.eg.db, ont = "all", pvalueCutoff =…

Aaltissimus

updated 3.8 years ago • SongW

Hi All Hope someone can help as it seems GSVA has some issues with other packages (that likely have been updated). After running...the test code below, an error is thrown "Error: [matrixStats (>= 1.2.0)] useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE

GSVA

updated 21 months ago • Alex

div class="preformatted">Hi All, I was wondering if anyone had any idea how one might put error bars on the log fold changes calculated by edgeR? I'd like to...could either be used to show the variance for each of the two conditions, or used to calculate an error for the fold change. but I'm a bit stuck as to how to actually implement this. Any ideas appreciated, Yours, Ian…

qPCR qPCR

updated 12.9 years ago • Ian Sudbery

into a group of other CEL files). It does not appear when operating on other CEL files independently. All files are hgu133plus2 chips. My setup: R 2.0.1 on Linux; latest version of affy (not devel) >abc<-ReadAffy() >cc<-rma(abc...Background correcting Error in density (x, kernel = "epanechikov", n=2^14) need at least 2 points to select a bandwidth automatically Erro…

updated 20.8 years ago • Min-Han Tan

div class="preformatted">I'm getting an error with R 2.0 devel, trying to install bioC devel. See below. It worked when I updated about a month ago but I tried last week...stat.math.ethz.ch. [1] "Installing reposTools ..." Loading required package: reposTools Error in getBioC(develOK = TRUE) : default: targets affy, cdna and exprs. exprs: packages Biobase, annotate, genefilte…

aCGH GO Biobase DynDoc annotate edd genefilter geneplotter rhdf5 multtest ctc ROC affy

updated 21.4 years ago • Matthew Hannah

Anders Greetings !! This is Vineeta Singh currently working on RNAseq data and got stuck in one error while using DEseq in estimateDispersion step error is given below . Its been wonderfull package but am unable to use...it. Please help me in resolving this error. I tried giving method type, fitType, sharingMode but all options failed. This data is simulated one in which ???A??? type are...cre…

RNASeq DESeq RNASeq DESeq

updated 11.7 years ago • Guest User

ppm= 20, peakwidth= c(20, 200)) Error in xcmsSet(c("./C12", "./C13"), method = "centWave", ppm = 20, peakwidth = c(20, : Chromatographic peak detection failed for all files! The first...error was: Error in mzR::openMSfile(x, backend = backend): Unable to create valid cRamp object. 此外: Warning messages: 1: In serialize

software error xcms

updated 5.4 years ago • 1227450726

I am using R version 3.4.1, Bioconductor 3.5 and RStudio to use scater package. I have 7 single-cell RNA seq datasets (from a 10x Genomics experiment), each corresponding to a different time point. Each dataset is a SCESet object. I want to merge the data all together. I have found there is the <span style="white-space:pre-wrap">`` mergeSCESet `` function. However…

scater single-cell

updated 8.4 years ago • nlehmann

div class="preformatted">I'm seeking advice on the use of the "all" component in various annotation data packages relative to GO. Using R version 2.4.1 and (e.g.) hgu133plus version 1.14.0...x <- as.list( hgu133plus2GO2ALLPROBES ) ##probe sets for each GO term xa <- unique( x[["all"]] ) ## holds probe sets associated to "all" xbp <- unique( x[["GO:0008150"]] ) # …

GO probe affy GO probe affy

updated 18.5 years ago • Michael Newton

of FASTQ files into R with the `ShortRead` package. It reads the first four files fine but gives an error on the fifth: ``` > test <- readFastq(buddy.file.list[[5]]) Error: Input/Output file(s): /sbgenomics/project-files/_5_buddy_0001.fastq...invalid character ' ``` Is the invalid character the single quote? Or is it not specified in the error message? There are sin…

shortread fastq

updated 6.3 years ago • lauren.fitch

been segmented and assigned regional p-values by GISTIC. (I have piles of other data that have all been converted to SummarizedExperiments now, because SEs rule). I'd like to slot them in with the rest of the data in a container...range or ranges. In order to not have the CNV results be obscenely large, I'd like to take all of the GRanges of each patient's segmented results, and use disjoin()…

updated 13.6 years ago • Tim Triche

Hi all, i am very new to bioconductor, and now i am planning to use TCGAbiolinks to download data from TCGA, in such case, the error...NCBI GEO/TCGA database")</pre> curl::curl\_download(input, tt, mode = "wb", quiet = !showProgress) error: Timeout was reached

tcgabiolinks

updated 9.8 years ago • maedakus

div class="preformatted">Hi all I've got the file test.R with the following code: filenames <- c("1M2W050304.CEL", "2M2W050304.CEL", "3M2W050304.CEL", "1M1W050304.CEL...Background correcting Normalizing Calculating Expression But then it comes with the error: Error in rma(ReadAffy(filenames = filenames)) : dimnames applied to non-array …

affy affy

updated 21.8 years ago • Jose Duarte

<div class="preformatted">The problem would appear to be in your data object, about which you give us no information. 1. There has been work on write.fit() recently. Try updating to the latest version from CRAN and see if the problem goes away. 2. In the latest versions of limma, you can also try write.table(fullfit, ...) 3. The problem is most likely that there is no component 'genes' i…

limma limma

updated 20.3 years ago • Gordon Smyth

div class="preformatted">All: I am getting an error message with GoHyperG (and a similar error with HyperGTable). library("hgu95av2") w1 <- as.list(hgu95avLOCUSID...myLL2 <- c(myLL1, sample(w2,100)) xx <- GOHyperG(myLL1,"hgu95av2",what="BP",universe=myLL2) Error: value for 'GO:0031997' not found > sessionInfo() Version 2.3.0 (2006-04-24) i686-redhat-linux-gnu …

drosophila2 cdf Biobase annotate genefilter multtest RBGL GOstats drosophila2 cdf RBGL

updated 19.4 years ago • Tony Long

The course materials for Dan Tenenbaum's course on "Bioconductor and Docker" [would seem to indicate](https://bioconductor.org/help/course-materials/2015/BioC2015/docker_and_bioconductor.html#using-shellinabox) that: (1) Bioconductor's AMI images all come with Docker installed and (2) appending \`:4200\` to the instance's RStudio URL will make it the instance's shellinabox URL...2015/BioC2015/doc…

ami

updated 10.1 years ago • joshmobrien

number and position by HG38. My data is named as df_1 and shown below. I get the coordinates of all the genes from database of HG38 by function like this: "txs <- transcriptsBy(TxDb.Hsapiens.UCSC.hg38.knownGene) " then...I use the findOverlaps with code: "df_overlap <- findOverlaps(df_1,txs)" but an error keep appear: Error in (function (classes, fdef, mtable) : unable to f…

func findOverlap

updated 3.9 years ago • Đạt

file (converted from paired-end bam file) by following the HelloRanges tutorial, but it gives me error while using `` eval ``: <pre> >code <- bedtools_coverage("-a 1.bedpe -hist -b org.genome") >code { genome <- Seqinfo(genome = NA_character_...cov <- unname(coverage(gr_b)[gr_a]) tab <- t(table(cov)) tab <- cbind(tab, al…

HelloRanges bedtools

updated 8.6 years ago • bioinf

div class="preformatted">Dear list, In the process of importing the ALL package into the Fedora repository [1] the reviewer has pointed out that the Licence tag in the description file does not...Could someone confirm me the license used and do the change accordingly in the next release of ALL? Thanks in advance for your help, Best regards, Pierre-Yves [1] https://bugzilla.redhat.com/show_…

PROcess PROcess

updated 14.6 years ago • Pierre-Yves

<div class="preformatted">Dear all, I am trying to use pamr.knnimpute with Agilent Microarray data which consist from 137 colums (samples) and 23653 rows (probes...div class="preformatted">Dear all, I am trying to use pamr.knnimpute with Agilent Microarray data which consist from 137 colums (samples) and 23653 rows...in log ratio, and 212 of them were "NA". I tried to run pamr.knnimpu…

Microarray pamr Microarray pamr

updated 19.0 years ago • washiot+1@gmail.com

KEGG pathways, still work and give results even after the new paid license and subscription like we all know the story. My question can be discussed in two different ways, I am wondering how people developing these packages...existing before privatization, as it was in public domain it is not going against the new license rules to distribute it. Regards Radhouane -- *Radhouane Aniba* *Bioinfo…

Pathways GOstats Pathways GOstats

updated 14.5 years ago • Radhouane Aniba

Dear all, Since December, an error has appeared in FELLA's release page. The error(s), affecting the vignette builds, is due to changes

fella software error

updated 6.0 years ago • sergi.picart

div class="preformatted">Dear All, I have a list of human genes with EntrezGene IDs. And I want to retrieve dN and dS values of them from biomaRt. I used the following...mmusculus_homolog_ds"), filters = c("entrezgene"), values= geneIDs, mart = ensembl) There is an error as the following: Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowe…

biomaRt biomaRt

updated 12.8 years ago • lemon tree

div class="preformatted">Hi all, I am getting this frustrating error in the 'affy' package, using the 'justMAS' function. I have looked at the function but cannot...figure out where the error comes from of how to fix it. x <- justMAS(cold.root.00.5.raw, tgt=100) Background correcting Retrieving data from AffyBatch...0.342672641420889 Scale factor for: CONTROL_30MIN_ROOT_REP2.cel 0.3…

updated 20.9 years ago • Dion Whitehead

dds <- DESeqDataSet(se, design= ~genotype + genotype:treatment) However I got the below error, which I was trying to track in the web but I found nothing. Error in checkSlotAssignment(object, name, value) : assignment...GenomicRanges_OR_GRangesList") is not TRUE I can not figure out what is going on. I updated all packages but the error still there. I downloaded the a…

deseq2 DESeqDataSet

updated 6.8 years ago • colaneri

div class="preformatted">hello all when i runned the scripts to clean the fastq data, it reported an error. but if i run it step by step, it has no problem reads &lt...fastqfile); seqs <- sread(reads); qual <- SolexaQuality(quality(quality(reads))) that is the error place: myqual_mat <- matrix(charToRaw(as.character(unlist(qual))), nrow=length(qual), byrow=TRUE) Err…

updated 13.8 years ago • wang peter

res,file='sim_condition_treated_results_deseq2.csv',sep = "\t",col.names = NA,quote = FALSE) error when running "dds<-DESeq(ddsHTSeq, betaPrior=FALSE)" : Error in designAndArgChecker(object, betaPrior) : full model matrix...is less than full rank all my txt files are as follows (i will paste the start and finish of an example file) : VIT_19s0177g003205 57 VIT_19s0177…

DESeq2

updated 4.8 years ago • polaxgr

Hi all, I am attempting to run DEXSEQ. When I run the command, "dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable...design=~sample + exon + condition:exon, flattenedfile=flattenedFile)", I have been receiving the error "Error in lf[[1]]: subscript out of .boundslattenedFile". I wanted to ask how to correct this issue. I have been using the following

software error

updated 5.6 years ago • huck.thornton

Dear all, I upgraded my WS with R 3.5.1 and EBImage version 3.8 and since than am having problems running script that were working..._IF015.R?dl=0 Data: https://www.dropbox.com/s/40e5tfohgdm9wlo/IF015\_plate002\_test.zip?dl=0 The error I get is coming from the computeFatures function:  Error in (function (..., deparse.level = 1)  :   number of rows of

ebimage image processing computefeatures

updated 7.2 years ago • Mathieu Gendarme

Hi all, I have salmon qunat.sf file when i tried to import i'm getting error reading in files with read_tsv1 2 3 4 5 6 Error in tximport...files, type = "salmon", txOut = TRUE, countsFromAbundance = "scaledTPM") : all(c(abundanceCol, countsCol, lengthCol) %in% names(raw)) is not TRUE salmon output looks like this. ```r Name Length EffectiveLength

tximport tximportData

updated 2.6 years ago • barrypraveen

biomaRt) #list to test broilers_HT.test<- broilers_HT$entrezgene #now I define my universe as all the entrezgenes all <- total_data_u$entrezgene # in your case, it's not all the entrezgenes, but those corresponding to the...options(digits=3) params_temp = new("GOHyperGParams", geneIds= broilers_HT.test, universeGeneIds=all, annotation="org.Hs.eg.db", ontology=…

multtest GOstats biomaRt multtest GOstats biomaRt

updated 16.0 years ago • Andreia Fonseca

div class="preformatted">Hi all, I am trying to install NOISeq package from Bioconductor using commands : source("http://bioconductor.org/biocLite.R") biocLite...NOISeq") But there is an error when installing: Warning message: package ?NOISeq? is not available (for R version 2.15.1) But in the manual it is mentioned

NOISeq NOISeq

updated 13.3 years ago • Fatemehsadat Seyednasrollah

Hi all,    I'm a new to arrayQualityMetrics, so hopefully this isn't an obvious question, but I've been getting the error below...acc=GDS961) and [GDS4012](http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS4012). The error I've received is: <pre> Error in x[pos] = log2(x[pos]) : NAs are not allowed in subscripted assignments Calls: runArrayQC ... platfo…

arrayqualitymetrics bugs error

updated 11.2 years ago • daugherty_a

div class="preformatted"> Dear all, I got this error while I was trying to normalize (first within arrays, then between arrays) Agilent arrays using these code...gt; > #########normalize between arrays > MA.b=normalizeBetweenArrays(MA, method="quantile") Error in xy.coords(x, y) : x and y lengths differ I found that MA$A and MA$M contain a few columns with all "NA" values. …

updated 21.2 years ago • Caimiao Wei

Dear all, I am trying to use the biomaRt package to access the data from Ensembl, however I got error message when using the useDataset...ensembl = useDataset("hsapiens_gene_ensembl",mart = ensemble) When I type useDataset function i got error message like this: > ensembl1 <- useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL",dataset = "hsapiens_gene_ensembl") Ensembl...site unre…

bioma biomaRt

updated 3.4 years ago • Riley Qiu

div class="preformatted">Hi All, I am pretty new to edgeR, this is the first time I use the package, as well as the first time I try to find differential expression...y <- DGEList(counts=x,group=group) > y <- estimateCommonDisp(y) and I get the following error: Error in if (mx < tol) { : missing value where TRUE/FALSE needed can anyone explain to me what the erro…

edgeR edgeR

updated 13.5 years ago • Lucia Peixoto

Hi I have been trying to use DiffBind to analyze our Chip-seq data and have been running into some errors repeatedly. I first created a samplesheet.csv describing my samples and it looks like this: SampleID,Tissue,Factor...minOverlap=3, bLowMem=TRUE) > H3K4.B73=dba.count(H3K4.B73, minOverlap=3, bLowMem=FALSE) And they all failed. My error in all three cases is as follows: Error in rea…

DiffBind DiffBind

updated 12.3 years ago • Anitha Sundararajan

downloaded_packages Old packages: 'checkmate', 'cluster', 'nlme', 'RcppArmadillo' Update all/some/none? [a/s/n]: a There are binary versions available but the source versions are later: binary source needs_compilation...Local\Temp\Rtmp8MmDrg\downloaded_packages But then when I try and load the library it gives an error (which I can't se…

s4vectors

updated 6.7 years ago • z.crane-smith

make: /envs/dada2/lib/R/share/make/shlib.mk: No such file or directory make: *** No rule to make target '/envs/dada2/lib/R/share/make/shlib.mk'. Stop. ERROR: compilation failed for package ‘DECIPHER’ * removing ‘/home

R bioconductor biocinstaller package installation

updated 7.4 years ago • ariel

div class="preformatted">Hi all, I?m attempting to QC a set of HGU133plus2 chips (n=20), using the simpleaffy package. ########################## > qc.data<-qc(celdata,my.eset) Getting...probe level data... Computing p-values Doing PMA Calls > plot(qc.data) Error in plot.window(xlim, ylim, log, asp, ...) : need finite xlim values ... ####################…

hgu133plus2 probe simpleaffy hgu133plus2 probe simpleaffy

updated 20.7 years ago • Larry La Pointe

div class="preformatted">Hi all, I was trying to use DESeq with the count table obtained from HTSeq- count. When I used the function "newCountDataSetFromHTSeqCount...it gave me an error complaining some lines of the count table do not have 24 columns. The error message looks like: "Error in scan(file, what

DESeq DESeq

updated 12.0 years ago • Xiaoyu Liang

load the oneChannelGUI package to analyse .CEL file microarray data but keep running into an error. I used: source("http://bioconductor.org/biocLite.R") biocLite(c("Biobase", "limma", "affylmGUI", "tkWidgets", "GOstats", "AnnotationDbi...oneChannelGUI","chimera", "cummeRbund")) to install the package and it returns this error: Error in data.frame(binary= binvers, source = srcvers,…

microarray software error bioconductor

updated 10.3 years ago • o.j.james

to solve this problem but couldn't. I'm using ```getBM()``` function of biomaRt but getting an error. I have used this code like 7 months ago without any error but now it's giving error and I think it should probably be because...bg_genes``` is around ~20000 gene ids. I tried with less gene ids (10) then it worked. The ERROR: ``` Error in getBM(attributes = c("go_id", "ensembl_gene_id", "…

go r software error R biomaRt

updated 5.6 years ago • morteza.aslanzadeh

div class="preformatted">Hi, I am working on the yeast2 affymetrix chip and am trying to filter out all the s_pombe probes with the following code: library(altcdfenvs) bothcdf = wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf...lt;- "envsaccdf" "s_pombe.msk" was downloaded from the Affymetrix website and contains a list of all the s_cerevisiae probes (those I want to use). This code runs wit…

yeast2 cdf yeast2 cdf

updated 17.7 years ago • Sebastien Gerega

<div class="preformatted">I am analyzing paired samples (RNA-seq). I am facing problem with edgeR at y <- estimateGLMTrendedDisp(d, design) step where it is saying error message "Error in t(y) + prior.count.scaled : non-conformable arrays" although it was ok with the step y <- estimateGLMCommonDisp(d, design) Apparently in the assignment step something is happening [design &…

Genetics Genetics

updated 12.0 years ago • Navonil De Sarkar

Hi, I have problem loading the bioClite and the ALL data set under the package "ALL". Here comes these warining messages:   > biocLite("ALL") BioC\_mirror: https://bioconductor.org...Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31). Installing package(s) ‘ALL’ installing the source package ‘ALL’ trying URL 'https://bioconductor.org/packages/3.4/data…

R ALL

updated 9.2 years ago • mdfislam89

div class="preformatted">*Hi,* *I am getting an error when trying to parse the latest msigdb version from Broad. I suspect the problem is due to Broad adding another category...be included in GSEABase? Is there a way to parse only categories c1-c6, or an alternative way to get all categories?* > gsc = getBroadSets("msigdb_v4.0.xml") *Error: 'getBroadSets' failed to create gene sets: …

Category Category

updated 12.2 years ago • Milica Ng

<div class="preformatted">Hi, I have used DEXSeq (version 1.2.0) successfully to find differentially expressed exons in RNA-seq data. Yesterday I upgraded DEXSeq to version 1.3.13 I get the following error: > ecs=read.HTSeqCounts(countfiles=file.path("/data/DexSeqCounts/",past e(rownames(samples),"txt",sep=".")),design=samples,flattenedfile...expressed exons in RNA-seq data. Yester…

DEXSeq DEXSeq

updated 13.5 years ago • Akula, Nirmala NIH/NIMH [C]

Dear all,  I am trying the tutorial of WGCNA in R-3.4.4. Everything seemed OK untill I try this command:      GOenr = GOenrichmentAnalysis...moduleColors, allLLIDs, organism = "mouse", nBestP = 10) It gives the following error:      Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : Object 'Ontology' not found Did y…

wgcna

updated 7.8 years ago • yepingsun80

div class="preformatted">Hi, all, When I ran LPE test on my 100 datasets, I got the following error message on two of the 100 tests. Can someone help me out of what...the possible cause(s) is? Thank you. "Error in var(M[vect.temp], na.rm = TRUE) : `x' is empty" The analysis failed at the step when "baseOlig.error()" was calculated. Best, Puhong

LPE LPE

updated 20.9 years ago • Puhong Gao

div class="preformatted">Dear all, On running the eBayes function, I got the following error. > fit_NODS7 <- eBayes(fit_NODS7) Warning message: Estimation...from the user. It worked for a couple of experiments and for the third set, gave the above error. Thank you, -Ankit</div

updated 20.7 years ago • Ankit Pal

Hey, earlier today/yesterday pathview code ran fine. Right now getting this error <pre> Error in UseMethod("select_") : no applicable method for 'select_' applied to an object of class "c('OrgDb', 'AnnotationDb...envRefClass', '.environment', 'refClass', 'environment', 'refObject', 'AssayData')" Error in `$<-.data.frame`(`*tmp*`, "labels", value = c("", "", "", "", : repl…

pathview

updated 7.6 years ago • Epic Tinus

My code is working fine on Ubuntu 14.04. But, when i migrated to Ubuntu 16.04, I get the following error for annotation with codelink package. The error comes when I select the annotation database. <pre> select(hwgcod.db, ......, c...SYMBOL"), "ACCNUM")</pre> __Error: __ <pre> Warning: Error in UseMethod: no applicable method for 'select_' applied to an object of class "c('…

codelink annotation ubuntu

updated 9.1 years ago • Agaz Hussain Wani

with respect to time series. However, if I try and perform the analysis you describe then I get an error when estimating the dispersions? do you know what is the cause and/or what I could be doing wrong? dds <- DESeqDataSetFromMatrix...dds <- estimateSizeFactors(dds) dds <- estimateDispersions(dds) gene-wise dispersion estimates Error in fitDisp(ySEXP = counts(objectNZ), xSE…

edgeR DESeq DESeq2 edgeR DESeq DESeq2

updated 11.9 years ago • Hickman, R.J. Richard

div class="preformatted">Dear All, When I am trying to perform mainAnalysis using RNAither. I get the below error. Please help me in overcoming this issue. Error

biomaRt RNAither biomaRt RNAither

updated 16.5 years ago • Kishor Tappita

Dear all, I have used CopywriteR package with sequencing data and got an error. Because I previously got a successful result with...Dear all, I have used CopywriteR package with sequencing data and got an error. Because I previously got a successful result with a different set of bam files, I think the problem would be the bam list (or some of the bam files), but I don't figure out what exact…

CopywriteR

updated 9.5 years ago • Tom

You must be wondering why error code 0X9A is bothering you and how you can get rid of it. Read this article; All your problems will be solved. To resolve [**Epson...printer error 0X9A**][1], apply the troubleshooting steps below. **Simple steps to know how to fix error 0X9A** Epson printer error 0X9A is a...software by following the instructions. After successful installation, open …

DFP

updated 4.4 years ago • evasmith09

div class="preformatted">Hi, I am encountering an error when running makeTranscriptDbFromUCSC() that was not occurring yesterday. I have tried on 2 separate computers/R versions...and get similar errors. Playing around, it seems like the function works for other genomes but not for hg19, which is what I am looking for. Any...gt; tx <- makeTranscriptDbFromUCSC(genome="hg19",tablename="…

genomes genomes

updated 12.0 years ago • Chris Cabanski

div class="preformatted">Hi all, I get this error when trying to run the gpQuality() function from the "arrayQuality" package for my GenePix microarrays (.gpr...files). > gpQuality() [1] "Starting gpQuality..." Error in if (abs(MMR[i]) > 0.5) numSpotOverMmrLim <- numSpotOverMmrLim + : missing value where TRUE/FALSE needed In addition: There...11 warnings (use warnings…

updated 11.5 years ago • Guest User