Bioconductor Forum

value is > [1] NA but with 2.9/2.4 I got the following error: > Error during wrapup: keys must be supplied in a character vector with no NAs This causes our pipeline to break there and stop the analysis while in the

Microarray Microarray

updated 16.7 years ago • Christian Kohler

function for annotations. I would like to be able to pass the GeneChip identifier to mget as a character string. Attempts to do this via "paste", as below, do not work because envir expects an object, not a character string

updated 20.3 years ago • Kimpel, Mark W

smallest number (decreasing order) keeping at the same time the first column that contains the gene names (=characters) since I need to know which gene is what after the other columns has been re-ordered. my dataset: # A tibble: 3 x 12...that works is selecting the numeric columns that I want to sort but in doing so I will lose the names of the genes: CD.sorted <- apply(tes…

sort R RNAseq character numeric

updated 5.3 years ago • camillab.

Sorry for the delay. On 01/19/2012 07:33 AM, Yuval Itan wrote: > Dear Herve, > > My name is Yuval, I am a postdoc at the Rockefeller University. I am trying to use Bioconductor for analyzing my RNA-seq data, and...got stuck. I need to count the number of reads per gene and my fastq data was aligned to chromosomes named "1", "2" etc. while makeTranscriptFromUCSC provided with…

Cancer TranscriptDb convert Cancer TranscriptDb convert

updated 13.9 years ago • Hervé Pagès

that respond to some treatment in different genotypes (wt vs ko). The genotype is described by the vector a <- c(1,1,1,1,2,2,2,2), the treatment by the vector: b <- c(1,2,1,2,1,2,1,2) and the batch effect (which is coming from the fact that the...same animal has been used in 2 samples) by the vector batch<- c(1,1,2,2,3,3,4,4) The effect of the batch is quite strong as it …

batch effect edgeR

updated 10.3 years ago • pavlidisp

with my labels ? The default is obviously the Block number, and I would like to replace it with my vector of labels (grlab, character), the same length of the number of the boxes. Yes I know that is more an R question, and even a stupid...on that !!! I tried with par() settings, axis(), adding "lab=", labels, tried to rename the xdata (names, rownames, etc). If someone could help me, it will be …

limma limma

updated 19.8 years ago • Giulio Di Giovanni

Input/Output file(s): /sbgenomics/project-files/_5_buddy_0001.fastq message: invalid character ' ``` Is the invalid character the single quote? Or is it not specified in the error message? There are single quotes in

shortread fastq

updated 6.2 years ago • lauren.fitch

fellow bioconductors, good afternoon. I am encountering an error concerning the allocations of vectors bigger than a certain size. My problem is that said size is far below the amount of RAM I have installed on the system...TRUE); # Extract expression data from lumi object: >Expression <- exprs(Data) >names(Expression) <- Data at phenoData@data$sampleID # Calculate…

Microarray lumi Microarray lumi

updated 15.7 years ago • Manca Marco PATH

Error in read.table(file = file, header = header, sep = sep, quote = quote, : 'file' must be a character string or connection If I use only one part of the list, all is good: peak=readPeakFile(Goettingen_peaks...peak, weightCol="V5") Error in .normarg_shift_or_weight(weight, "weight", x) : 'weight' must be a numeric vector, a single string, or a list-like object any…

ChIPseeker readPeakFile

updated 6.6 years ago • theodore.georgomanolis

Hello, I am a new user of the package NanoStringDiff. I am working on an experiment with 4 groups and I am trying to figure out how to design the contrast vector, **specifically which numbers to use for each group**. To the best of my understanding, "0" omits the group, and the numbers, "1...I am working on an experiment with 4 groups and I am trying to figure out how to design the contrast ve…

NanoStringDiff

updated 3.0 years ago • Paraskevi

I notice that in the ballgown constructor there is an option to enter a "bamfiles" vector, as described in the ballgown manual here: __bamfiles                optional vector of file...t understand what the use for this is though.  I do have bam files, but if I just leave this vector as NULL, am I losing some downst…

ballgown

updated 7.3 years ago • jac1318

version assays(1): counts rownames(52): Otu00001 Otu00002 ... Otu19614 Otu32323 rowData names(0): colnames(20): BP1 BP1P ... BP7 BP7P colData names(9): Sample.ID Age ... Experiment.Number Type coldata <- colData(dsq) > head...Sample.ID Age Time.Point Treatment Sex Status Animal <character> <…

DESeq2

updated 22 months ago • DS

S)<-c("MEST","INHBA","IGF2","H19","GNAS","GRHL1","SNPRN","MEG3","PEG10","CDKN1C") multiData =vector("list",2) multiData[[1]] =list(data= R) multiData[[2]] =list(data= S) names(multiData)=c("Ref","SGA") checkSets(multiData, checkStructure...FALSE, useSets = NULL) multiColor =vector("list",2) multiColor[[1]] =c('blue',"blue","red","red","grey","tan","tan","purple","grey","pu…

wgcna

updated 6.7 years ago • maya.kappil

see that keys used for lookup are well formed (e.g, there are no NA or NULL values and all keys are character), and more importantly returns an error message that clearly states what the problem was. The second point is more...env=hgu133plus2ENTREZID,ifnotfound=N A))) > Error in .checkKeysAreWellFormed(keys) : > keys must be supplied in a character vector with no NAs > &am…

Microarray Annotation hgu133plus2 hgu95av2 AnnotationDbi Microarray Annotation hgu133plus2

updated 16.7 years ago • James W. MacDonald

The readVcf function apparently works fine on phase 3 1000 Genomes data (see output at the bottom). However, when I try to use some functions mentioned in the manual, I get various error messages.  head(rowRanges(vcf), 3) Error in head(rowRanges(vcf), 3) :    error in evaluating the argument 'x' in selecting a method for function 'head': Error in rowRanges(vcf) :…

variantannotation readvcf

updated 10.6 years ago • pifferdavide

Hi, Following an old vignette on "How to use clusterProfiler to do GO enrichment analysis with unsupported organisms" I've got this error.  library(clusterProfiler) > Gff2GeneTable("all.gff3", compress=T) Reading all.gff3: found 813788 rows with classes: character, character, character, integer, integer, character, character, character, character  __Error in mer…

clusterprofiler go Gff2GeneTable buildgo unsupported organisms

updated 9.1 years ago • Didi

X4_Frozen,X11_RNAlater,X12_RNAlater,X13_RNAlater,X14_RNAlater)) #X1_Frozen etc. = equals row names/groups design = model.matrix(~0+cond) design = model.matrix(~0+cond) colnames(design) = gsub("cond","",colnames(design)) contrast...error message: Error in makeContrasts(contrasts = x, levels = design) : The levels must by syntactically valid names in R, see help(m…

limma

updated 5.4 years ago • mjensen2

in GAlignments(seqnames = bamcols$rname, pos = bamcols$pos, cigar = bamcols$cigar, : 'seqlengths' must be an integer vector with unique names In addition: Warning message: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels

software error easyrnaseq genomicalignments bam

updated 10.2 years ago • Michael Dondrup

method of subsetting you are using (dimensionless subsetting) coerces the result to be an ordinary vector. Hence any attributes such as rownames must be lost because vectors don't have rows or columns. This is how R works, and...it has nothing particularly to do with limma. If you want to preserve rownames, you must treat the object as a matrix, i.e., you must treat it as having two dimensions…

Annotation affy limma Annotation affy limma

updated 19.6 years ago • Gordon Smyth

I'm running goseq on a sequence of bootstraps where a DE test is performed on a random selection of replicates. THis way, I have a constant list of background genes and a selection of significant genes which is slightly changing from bootstrap to bootstrap. goseq works nicely on most of these bootstraps, but every now and then it crashes. Here is an example: <pre> > library(goseq) …

goseq

updated 10.9 years ago • M.Gierlinski

following error when running a specific dataset module <- runFastHeinz(subnet, scores) Error in names(best.path) <- names.list : 'names' attribute [18] must be the same length as the vector [6] -- output of sessionInfo(): R version 3.1.0

updated 11.6 years ago • Guest User

Hi, after performing this code sigCpGs <- DMPs$Name[DMPs$adj.P.Val<0.05] length(sigCpGs) [1] 311082 all <- DMPs$Name length(all) [1] 870529 par(mfrow=c(1,1)) gst <- gometh(sig.cpg...the argument 'x' in selecting a method for function 'grepl': $ operator is invalid for atomic vectors or if I use minfi created object `annEPICv…

DNAMethylation GO MethylationArray missMethyl EPICv2

updated 22 months ago • saad.malik

preserved in counts(dds) estimating dispersions Error in `rownames<-`(`*tmp*`, value = names(x)) : duplicate rownames not allowed Of course I checked rownames are unique: > rn = rownames(dds.ed) > rn[duplicated(rn...character(0) Also tried setting new rownames like `` rownames(dds) = 1:length(dds) ``, but I still get this error. I've tri…

software error deseq2

updated 7.2 years ago • ashley.doane

classes, fdef, mtable) : unable to find an inherited method for function ‘select’ for signature ‘"character"’ `` Any suggestions to solve this? Thanks, Guido   <pre> > library(affyPLM) > affy.data <- ReadAffy() > > x.norm &lt...classes, fdef, mtable) : unable to find an inherited method for function ‘select’ for signature ‘"chara…

annotation organismdb

updated 9.3 years ago • Guido Hooiveld

R for DeSeq2 analysis but I can't seem to get the first column of my colData to match the column names of my countData. The match (vector 1, vector 2) function isn't working and I think it has to do with the layout of my data. The

deseq2 bioconductor

updated 6.8 years ago • ishtarredman

I thought I saw a mention on the mailing list that coverage and similar functions would support a named vector for providing the width instead of just a list. The documentation states so too: For RangesList and RangedData...objects, a list or vector of the same length as ?x? to be used for the corresponding element in ?x?. However, using a named vector does not work (my aln.…

Coverage Coverage

updated 13.5 years ago • delhomme@embl.de

Now when running the script on multiple concatenated sequences, I get the error "Illegal characters found in URL". I've traced the error back to this line of the function: post <- htmlParse(getURL(url0, followlocation...of the getURL call to handle https. It looks as though the getURL function doesn't handle the \\n character in the same way. Thoughts on how to fix this? A quick …

blastsequences getURL

updated 9.0 years ago • dansmaynard

topTable() in limma packages returns the row numbers and it would be useful to see the row names (i.e. Affy ID) instead. I am aware that I may supply the 'genelist' argument but help("topTable") says : genelist: data frame or...character vector containing gene information. If not specified, this will be taken from the 'genes' component of 'fit'. My us…

affy limma affy limma

updated 20.8 years ago • Adaikalavan Ramasamy

Summits on  Un0097  ..</span>_ _<span style="background-color:transparent">Error in names(res) <- nms :</span>_ _<span style="background-color:transparent"> 'names' attribute \[20\] must be the same length as the vector...fictitious chromosome called "chromosome unknown" which accounts for the "Un" part of the chromosome name.</span

ChIPQC chip-seq

updated 8.1 years ago • nbkingsley

Hi, I am trying to add gene names to match ensembl gene ID, below is the code and the error. Any suggestions will be good. Thanks a lot! genemap=getBM(attributes...The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this on the support site at http://support.bioconductor.org

biomart

updated 5.7 years ago • xiaolei.zhou

How may I change the row names of an assay to make it more compatible with other R analysis? ``` > class(cancerAssays) [1] "MultiAssayExperiment" > assay...unable to find an inherited method for function 'assay<-' for signature '"MultiAssayExperiment", "character"' ``` It seems to me that the assay data is not overwriteable

MultiAssayExperiment

updated 5.2 years ago • Dario Strbenac

184 / 300  213 / 300  243 / 300  272 / 300  300 / 300 Error in names(res) <- nms :   'names' attribute \[18\] must be the same length as the vector \[1\] Calls: ChIPQC -> bplapply -> bplapply -> bplapply

ChIPQC

updated 8.5 years ago • seasky002002

the DESeq2 pasilla dataset example, but not for my own data, which gives an error: ``` Error in names(ls.mean) <- sapply(nam, paste) : 'names' attribute [2] must be the same length as the vector [0] ``` It's not clear to me where in the vsBoxPlot

vidger

updated 5.5 years ago • bbj23

relationship final dispersion estimates, fitting model and testing: 14 workers Error in vector(mode(x), length(NArows)): vector: cannot make a vector of mode 'S4'. Traceback: 1. DESeq(dds, test = "LRT", reduced = ~gene_target, fitType...mcols(objectNZ), mcols(object)$allZero) 4. DataFrame(lapply(resultsList, function(x) vector(mode(x), length(NArows)))) 5. lapp…

deseq2

updated 7.4 years ago • ben.langmead

When I used ChIPQC, I followed the manuals to construct a sample sheet (name is "examplefile.csv"), and then run: >a <- read.csv("examplefile.csv") >b = aa = ChIPQC(a, annotation=NULL) air\_k14\_2 air\_k14...When I used ChIPQC, I followed the manuals to construct a sample sheet (name is "examplefile.csv"), and then run: >a <- read.csv("examplefile.csv") &am…

software error bioconductor chipseq chipqc

updated 10.4 years ago • wangzhe335

vcf)$ALT, which returns a DNAStringSetList. Each element contains a DNAStringSet with one or more characters (there are tri-morphic SNPs in this data set). I would then like to write this to a new file, concatenating the allele...1\]\] A \[\[2\]\] C \[\[3\]\] A G \[\[4\]\] T \[\[5\]\] A C T \[\[6\]\] A to this character vector: \[1\] "A"     "C…

readVcf DNAStringSet DNAStringSetList variantannotation readvcf

updated 10.7 years ago • dan.gatti

now try to modify the positions nodeNames <- nodes(g1) nNodes <- length(nodeNames) nodePos <- vector("character", nNodes) names(nodePos) <- nodeNames nodePos[1:nNodes] <- c(".15,.15",".25,.25",".35,.35",".45,.45",".55,.55") # note I have tried the above...position, see: http://www.graphviz.org/pub/scm/graphviz2/doc/info/attrs.html#a:pos z <- agopen(g1,nam…

graph Rgraphviz graph Rgraphviz

updated 15.5 years ago • Robert M. Flight

Sheet1", phenoDataDccColName = "ROI_ID", protocolDataColNames = c("Segment Tag", "Scan Name")) ``` Output: Error: `path` must be a string # please also include the results of running the following in an R session sessionInfo

HELP path

updated 17 months ago • cpierce2

run this, it comes up with "Error in .local(.Object, ...) : allGenes should be a factor or a numeric vector" [This][2] is what my gene list looks like (entrez ID as row names and adjusted p values down the column versus [their example

topGO topgo GO term analysis

updated 5.4 years ago • ccha

<div class="preformatted"> Hi Could someone please help me out with this error on a hyperGTest with KEGG parameters? I get the same error on the hgu133plus2 chip. Must be something wrong with my parameter definition but I can't work out what. > params<-new("KEGGHyperGParams", geneIds =entrez_set0.05...with this error on a hyperGTest with KEGG parameters? I get the same error…

Annotation GO hgu133plus2 moe430b mouse4302 Annotation GO hgu133plus2 moe430b mouse4302

updated 16.7 years ago • John Coulthard

div class="preformatted">Hi All, How can I create a variable with a name identical to the character value of an argument that I passed to the function ? The following lines doesn?t work. Do I have

updated 11.4 years ago • my1stbox

I have some bam files with chromosome names like "1" instead of "chr1". I run into problems when I want to plot data from ensembl along with coverage data from these bam...to modify the function that reads data from the bam file somehow so that it returns the chromosome name prefixed with "chr". Is that possible? I tried editing the default import function, only editing the line giving seqnames..…

gviz

updated 9.0 years ago • stianlagstad

div class="preformatted">Hi list, I am trying to call makeContrasts() in limma to accept character vector of all samples vs control. But it seems that makeContrasts() consider only the first element in the contrast...vector. Basically what I've done is first to assign design matrix "dMatrix", then make a contrast character vector "con" using paste...of what I'm doing wrong would be appreciat…

limma ASSIGN limma ASSIGN

updated 18.2 years ago • Amin Moghaddasi

group, > Apologies for asking the most chomped FAQ. > > I have a file with list of gene names(genes.txt): > EGF > EGFR > PTPN6 > TIEG2 > MAPK1 > > > I have another object in R, I do not know the data > type for that...object. > > Is it because that lidnames is as a list type and > mygenes obje…

convert convert

updated 21.4 years ago • Adaikalavan Ramasamy

example > CpH.fwd = with(CpH, GRanges(chr, IRanges(end=site,width=50), strand=CpH.strand, names=rownames(CpH))) > CpH.fwd GRanges with 3091 ranges and 1 elementMetadata value: seqnames ranges strand | names <rle> <iranges...rle> | <character> [1] chrX [ 7556494, 7556543] - | ch.X.7566543R …

BSgenome BSgenome BSgenome BSgenome

updated 14.2 years ago • Tim Triche

div class="preformatted">Dear all, I observed this problem regarding the maximal length of a Rle vector: > rle = Rle(rep(0, 1000000000)) > length(rle) [1] 1000000000 > length(c(rle, rle, rle)) [1] -1294967296 Probably, it is caused by the...I used the coverage() method and then concatenated all chromosomes. This should give me an Rle vector of length ~3*109, but mean…

Sequencing Sequencing

updated 14.1 years ago • Hans-Ulrich Klein

pre> gff <- import('hsa.gff3') hairpin <- gff[mcols(gff)$type == 'miRNA_primary_transcript',] names(hairpin) <- mcols(hairpin)$ID mature <- gff[mcols(gff)$type == 'miRNA',] names(mature) <- mcols(mature)$Derives_from mature_relative...lt;- shift(mature, -start(hairpin[names(mature),])) names(mature_relative) <- mcols(mature)$ID</pre> Thi…

genomicranges

updated 10.1 years ago • Jake

files are ( mine or GEO one that had worked fine), now I always see an error as "All the CEL files must be of the same type. Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE".... So I'm wondering if anyone has...NetAffx Annotation... OK Done. Warning messages: 1: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(x) : is.na() applied to non…

BiocViews Annotation Organism biocViews oligo BiocViews BiocViews Annotation Organism

updated 14.6 years ago • Setsuko Sahara

https://genome.ucsc.edu/cgi-bin/&quot">https://genome.ucsc.edu/cgi-bin/&quot</a>;) Error in names(trackIds) <- sub("^ ", "", nms[nms != "new"]) : 'names' attribute [210] must be the same length as the vector [209]</pre> Indeed if I tried to list the...message <pre> supportedUCSCtables(genome="hg19", url="http://genome.ucsc.edu/cgi-bin/") Error i…

software error genomicfeatures

updated 7.7 years ago • rmendez

txdb <- makeTxDbFromGFF(gtffile, format="gtf", circ_seqs=character()) ebg <- exonsBy(txdb, by="gene") se <- summarizeOverlaps(features=ebg, reads=bamfiles, mode="Union", singleEnd=TRUE, ignore.strand...when testing validity of SortedByQueryHits object returned by subsetting operation: 'queryHits(x)…

summarizeOverlaps genomicalignments

updated 9.4 years ago • philipp.wahle

dirs) tmp=sapply(strsplit(batchNames,"\\."),function(x) as.numeric(x[1:2])) files=vector("list",length(dirs)) ngenes=27578 for(i in seq(along=dirs)){ tmpPath=file.path(homedir,dirs[i]) fns=list.files(tmpPath) files...betas=matrix(b,nrow=ngenes,ncol=sum(nfiles)) betas=matrix(NA,nrow=ngenes,ncol=sum(nfiles)) cnames=vector("character",sum(nfiles)) batch=factor(rep(seq(along=files),nfiles)) fo…

updated 14.0 years ago • Magdalena Wozniak

q.norm, remove.category="Undetermined", n.category = 36, remove.name=c(HK.miR.rm,"MammU6")) Error in names(x) <- value : 'names' attribute [41] must be the same length as the vector [0] > traceback() 6: `colnames<-`(`*tmp*`, value = c("C1", "C2", "C3", "C4", "C5...paste("A", 1:n, sep=""), featureCategory=as.data.frame(array("OK", c(n,n)))) > raw[,1] Error in names(…

HTqPCR HTqPCR

updated 14.8 years ago • Wenbo Mu

<div class="preformatted">hello All, I was wandering if you could possibly give me some suggestions with the following problem: I would like to build a pipline which opens consequently exprset files (imported from GEO) and extracts and evaluates the phenoData labels (except the fields "sample" and "description"). The program is below: the basic problem is that when you use names(pData(eset…

updated 18.5 years ago • Sergii Ivakhno

x=ss_beads, y=bc_ms) **Error in vapply(bc_ms, function(x) which(ms == x), numeric(1)) : values must be length 1, but FUN(X[[2]]) result is length 2** I noticed that the ss_beads@parameters@data[["name"]] is a character where as for the...ss_exp@parameters@data[["name"]] it is a factor. I tried to change it to a factor, but this didn't seem to help. ss_beads@parameters@data[["name"]]…

CATALYST flowCore assignPrelim Error in vapply read.FCS

updated 6.9 years ago • j.krop

2.0 ST array data and would like to send the expression of the gene with MGI Sybmol "Ly76" (common name: Ter-119) to collaborators. However, I can not seem to find it on the entire array - is this possible, or does something go wrong...library(oligo) library(annotate) library(mogene20sttranscriptcluster.db) \# celFiles is a character vector with file paths: affyRaw <- oligo::re…

pd.mogene.2.0.st mogene20sttranscriptcluster.db annotate

updated 8.4 years ago • felixwertek

the filter cannot be found? At least when annotating your results you'd be able to get same length vectors, and it would be much easier to do that in data.frames. thanks for any suggestions, cheers, Francesco On 29 Aug 2013, at...other chips I do this: ID <- featureNames(AF.eset.RMA) Symbol <- getSYMBOL(ID, 'mouse4302.db') Name <- as.character(lookUp(ID, "mouse4302.db", "GE…

annotate biomaRt oligo annotate biomaRt oligo

updated 12.3 years ago • Lescai, Francesco

use logical operators, such as XOR and intersect, but I found that all these operators are for two vectors only. Does anybody know if there is operator functions for several vectors. To explain my problem more clearly, here

updated 14.8 years ago • Wendy Qiao

I have some issue while passing contrast argument as a vector. I create a vector <pre> contrasts <- c("TT-C,D-C,DT-C,D-TT,DT-TT,DT-D")</pre> after removing double quotes from the above vector by

r limma differential expression

updated 10.5 years ago • Agaz Hussain Wani

I want to split into multiple BAM files, based on the "_tags_" that I have appended in the read names (so __qname__ param) . I thought it might be possible using \``` Rsamtools::filterBam() ``\`  function if I am able to provide the...expect a single DataFrame argument representing all information specified by param. Each function must return a logical vector, usually of length equal to …

rsamtools

updated 10.0 years ago • Vivek.b

to avoid intercept colnames(design) <- c('Cont','Test') ## Personalize the design with col names # fit <- lmFit(exprs(esetRMA), design) fit <- lmFit(exprs(esetRMA), design) contrast.matrix<-makeContrasts(Test-Cont, levels...fit2, coef = 1, adjust = "BH", number = 50) Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a v…

Normalization affy limma convert Normalization affy limma convert

updated 12.7 years ago • Atul Kakrana