Bioconductor Forum

version that I am using is 2.15.0 The input for the function was eset and for the intgroup argument character vector "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 ses…

updated 13.6 years ago • Guest User

results from a mgug4122a Agilent microarray. Summary of the problem is as follows: I have two vectors: DE_gr_iii and ALL_gr_iii (created following the SPIA vignette, see below). > class( DE_gr_iii ) [1] "numeric" > class( ALL_gr_iii...1] "character" > names( DE_gr_iii ) <- ALL_gr_iii > DE_gr_iii[1:10] 12808 78369 71897 241568 10207…

Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism

updated 15.6 years ago • January Weiner

expression <- cbind(expression, rrM.ProfileData)</pre> The following is my function genes is a character vector containing names of the desired genes. cancer is also a character vector string containing names of desired...library("cgdsr") mycgds = CGDS("http://www.cbioportal.org/") colname <- vector("character", length(cancers)) colname[1] <- "Gene.nam…

loop matix

updated 9.9 years ago • Arman Shahrisa

<div class="preformatted">Hello Bernd and BioC people: Writing empty character strings results in a C-level HDF5 error starting in rhdf5 2.8.0. See transcript below, under 2.8.0 (I am not attaching the transcript under 2.7.3, where it works fine). I didn't test if this is specific to character or would happen with other types. I noticed in NEWS the note "h5createDataset automatically uses…

updated 11.5 years ago • Brad Friedman

Hi All, I have performed a differential expression analysis using DESeq2, and would now like to analyze enriched GO terms using the topGO package.  However, I am having difficulty formatting the gene names for input.  Here's what I have so far. <pre> ## create named vector of p values GO_genes = setNames(res$padj, row.names(res)) ## create a gene selection function …

topgo biomart deseq2 gene ontology

updated 8.6 years ago • krc3004

keyType = "ENTREZID") **Error in .testForValidKeys(x, keys, keytype, fks) : 'keys' must be a character vector

clusterProfiler

updated 3.5 years ago • ltb47

error message when I was creating a flowSet consisting of two .lmd files.  <pre> Error in names(from) <- paste("V", seq(1, length(from)), sep = "") : 'names' attribute [2] must be the same length as the vector [0] </pre> My entire workscreen...0' as default. > x flowFrame object 'JennyG4a23052015.LMD' with 50000 cells and 6 observables: name …

lapply

updated 10.1 years ago • Wilson Yeo

following error: Error: 2 errors; first error: Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL' I have included the complete output of my attempt to run the vignette...with SYMBOL... Error: 2 errors; first error: Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type…

Microarray Annotation Preprocessing hgu133plus2 hgug4112a virtualArray Microarray hgug4112a

updated 11.5 years ago • Guest User

div class="preformatted">Hi, all, I want to randomly shuffle sample names in an object of expressionSet, aiming to perform permutation test. I did as follows, but the following test result remained...unchanged (When I shuffled the original data file names before 'ReadAffy()' , the result did change). So it must be wrong; what's the way please? Thanks to everybody who help / has helped...filen…

updated 17.1 years ago • Al Tango

bin score expCount expNums expScores <rle> <iranges> <rle> | <character> <character> <character> <character> <character> ZBTB33 chr1 10074-10329 * | 585 354 2 204,246 354,138 CEBPB chr1 …

genomicfeatures

updated 6.8 years ago • rodolfobahamonde

and br.out$fitted to be of length 2700 corresponding to the columns of single\_cell\_experiment. The vectors are the right length, but I noticed the labels of the output vectors don't match the input SCE (or each other): <pre> > head...barcodeTotal <character> <character&g…

dropletutils

updated 7.0 years ago • jmanning

the following error message. I believe it might be at the estimateDispersions step. "Error in names(res) <- nms : 'names' attribute [16] must be the same length as the vector [1] Calls: estimateDispersions ... estimateDispersions

software error

updated 5.4 years ago • huck.thornton

a .csv file as an input, but keep getting the error: | | | 0% | |=========== | 22%Error in names(comp)\[1\] <- "value" : 'names' attribute \[1\] must be the same length as the vector \[0\]< I am following the formatting that is given

PAPi

updated 8.9 years ago • k_hulce

ask = FALSE, lib = 'output/software/r/package/installation/')</pre> where listOfBiocPackages is a vector of characters with names of Bioconductor packages. If I update listOfBiocPackages, it is going to reinstall all the

bioclite package installation installation install

updated 7.9 years ago • cristian

Hello! I having some difficulties to convert a S4 vector to a vector in the shortRead package. I simply would like to trim the sequences contained in a shortReadQ object and...their associated quality scores based on a vector (filterTable$start). Such as: <pre> # Read the fastq file <…

shortread

updated 9.4 years ago • Radek

div class="preformatted">## Count probes mapping to top-node offspring ## ## probes - a character vector of probe IDs ## ## probeType - the annotation package type (no trailing ".db") of the ## probe IDs ## ## ontology - one of "all", "BP...CC", or "MF". ## ## topNodes - a list named by the GO ontologies ("BP", "CC", "MF") where ## each element is a character vector of GO IDs to be used as a t…

Annotation GO probe Annotation GO probe

updated 16.1 years ago • Seth Falcon

details:   call: match.arg(synchronous, c("off", "normal", "full"))   error: 'arg' must be NULL or a character vector Error: package ‘GO.db’ could not be loaded   > library(GO.db) Error : .onLoad failed in loadNamespace...details:   call: match.arg(synchronous, c("off", "normal", "full"))   error: 'arg' must be NULL or a char…

GO.db loadnamespace annotation chippeakanno

updated 10.8 years ago • adrianna-christina

only 2 reps (not with 3) and with hu95 chips with 3 replicates. The error msg is: >Error in "names<-.default('*tmp*', value = c("100_g_at", "1000_at", >"1001_at", : 'names' attribute [12625] must be the same length as the >vector [12551...probes with identical ranks and when the ranks are sorted, some are equal so they drop out, but the names vector is still the same…

siggenes siggenes

updated 20.2 years ago • Ken Termiso

I was able to read a tabix file, including the first line that started with # and had column names. Now with Rsamtools 1.8.4, it skips that line and the first element of the character vector is the first record of the tabix...file. Any way to get the old behaviour back so that I can know the column names ? anno <- "http://genomesavant.com/savant/data/hg18/hg18.refGene.gz" txTabix <…

updated 13.6 years ago • Dario Strbenac

columns: seqnames ranges strand | gene_id gene_type transcript_id <rle> <iranges> <rle> | <character> <character> <character> [1] chr1 11869-12227 + | ENSG00000223972.5 transcribed_unproces.. ENST00000456328.2 [2] chr1...ENSG00000223972.5 transcribed_unproces.. ENST00000450305.2 transcript_type exon_id exon_number <character> <charac…

branchpointer

updated 3.9 years ago • alexandre.maucuer

FALSE, + indicate = c("condition", "replicate"),plot=TRUE) Error in names(cols) <- var : 'names' attribute [7] must be the same length as the vector [2] I have used the same data for generating pca plot and

dep

updated 5.6 years ago • nkvnambiar

Dear all, I have bed files with ChIP-seq data, with sequence (chromosome) names like this: chr1, chr10, chr11, chr12, chr13, chr13\_random, chr14, . . ., chrX I  import the bed file data into a DiffBind DBA object...Dear all, I have bed files with ChIP-seq data, with sequence (chromosome) names like this: chr1, chr10, chr11, chr12, chr13, chr13\_random, chr14, . . ., chrX I&nbs…

DiffBind ChIP-Seq

updated 11.1 years ago • Georg Otto

here: http://grokbase.com/t/r/bioc-devel/141cegqvpf/no-method-for-coercing- this-s4-class-to-a-vector The error message is: Error in as.vector(x) : no method for coercing this S4 class to a vector In my case, however, I'm using...in NAMESPACE and this Depends: BiocGenerics in DESCRIPTION. It still does not work. I must be missing something. Any help is highly appreciated! Thanks Ninni -…

updated 11.3 years ago • Guest User

documentation (Textual description of affy vignete and ?ReadAffy) indicates that I need to set up a character array with both the file-names and the desired sample- names. This is what I have used (limited data-set for testing...the purpose of the sampleNames argument? Or ss there another way of changing the "column" names in an eSet and in write.exprs() output? Any suggestions much appreciate…

affy affy

updated 22.5 years ago • Paul Boutros

Call2("Rle_getStartEndRunAndOffset", x, start, end, PACKAGE = "IRanges") : 'x' values larger than vector length 'sum(width)' This only happens when I am trying to summarize reads according to genes. For count = "transcripts", everything...annotation object myself, since I could not find any other way to get an annotation object with gene names and not only transcript names from UCSC. I did thi…

RNASeq Annotation Organism BSgenome BSgenome easyRNASeq RNASeq Annotation Organism

updated 13.3 years ago • Guest User

ConfFile which says the following- Error in convertWellCoordinates(slog$Well, pdim(object)) : 'x' must be either a character vector with alphanumeric well IDs (e.g. 'B03' or c('B', '03')) or a vector of integers with position IDs within

cellHTS2 cellHTS2

updated 17.9 years ago • dunicadj@tcd.ie

an error while using the topTable from limma: Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type I checked all the steps that might be causing the error but couldn't find out...ExpressionSet (storageMode: lockedEnvironment) assayData: 45101 features, 12 samples element names: exprs protocolData sampleNames: 00.0A.CEL 00.0B.CEL ...…

updated 12.7 years ago • Atul Kakrana

created an object of 3'-UTRs and can export them as gff. But I would like to also include the gene names in the gff-file. They are there in the column Name, but i don't know how to include this in the gff-file. My script: <pre> txdb = makeTxDbFromGFF...utr) export(utr, "3_UTR.gff", format = "GFF")</pre>   I would like to also have the gene names under the column Name to…

rtracklayer gff

updated 8.8 years ago • Jon Bråte

I have this function and sometimes it gives me error: <code>refGenes <- UcscTrack(track="RefSeq Genes",                         table="refGene",                   &nbsp…

givz UcscTrack

updated 9.3 years ago • shuoguo

my design, I'm unsure of the DESeq2 interface for querrying it for results given that I can't use name=... anymore with "Group_GroupA_vs_GroupB". It looks like just a name ("GroupGroupA") is testing for difference in the means between...c("GroupGroupB")))) ``` type description <character> <character> …

DESeq2

updated 5.1 years ago • thadryan

Hi, I want to use reutils to obtain the accession numbers of a query search in character format. When I use efetch, the accession number isn't in a character format, and I'm not sure if the number is accurate

R

updated 8.6 years ago • ezrabekele17

Hello! When I used dba.analyze() with my DBA object linking to bam files, I got errors. My command was as below. ``` anaScramblecst <- dba.analyze(Scramblecst) ``` It returned the errors *" No matching chromosomes found for file: ..bam" and "Blacklist error: Error in BamFile(file, character(0)): 'file' must be character(1) and not NA"* Then I tried ``` Scramblecstbl<-dba.blackli…

DiffBind

updated 5.0 years ago • ahua217

pre> DESeqDataSet(se, design = ~ condition)</pre> Where "condition" is the actual column name. I'd like to have the column name be adjustable. I tried using a variable in the formula: <pre> design_col = "condition" DESeqDataSet...design_col)</pre> As might be expected, that does not work ("all variables in design formula must be columns in colData"). I then tri…

deseq2 r design matrix

updated 9.4 years ago • igor

two or more exons (this is long read RNASeq data). However, I am getting an error when providing a character vector of CIGAR values associated with the alignment. "Error in .fillWithDefaults(DataFrame(chromosome = as.character...elements in argument 'cigar' is invalid" my BAM file contains the same number of lines as the cigar character vector so I am not sure what the issue is? If i generate …

gviz

updated 9.3 years ago • d.depledge

is the workhorse behind pileLettersAt(). ### 'x', 'pos', 'cigar': 3 parallel vectors describing N strings aligned ### to the same reference sequence. 'x' must be an XStringSet (typically ### DNAStringSet) object...the unaligned strings (a.k.a. the ### query sequences) reported with respect to the + strand. 'pos' must ### be an integer vector where 'pos[i]' is the 1-based position on the ### refer…

SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP

updated 12.2 years ago • Hervé Pagès

div class="preformatted">Hi, Please see the code below this message. 'a' is a vector, 'b' is a scalar. But their types are show the same ('numeric'). If I use 'class()', I will not be able to tell the type difference between...a vector and a scalar. I am wondering if there is any other command that can tell the type difference between a vector and a scalar

updated 16.4 years ago • Peng Yu

Error in data.table::fread(input = mutsig, sep = "\t", stringsAsFactors = FALSE, : input= must be a single character string containing a file name, a system command containing at least one space, a URL starting 'http

maftools mutsig

updated 6.8 years ago • rina

I am interested to know how can i access vector of a column in phenotype data frame if  i don't know the conditions(groups) name in the phenotype data frame . I have...design <- model.matrix(~0+f) colnames(design) <- unique </pre> Now i don't know the column name of conditions(groups), how to access and design a model matrix. Help appreciated

r limma

updated 10.5 years ago • hashmi

Cn 1 3 t0 41742 .... how can I make read.targets() use my first targets column to define the row names, and make them available (as t0Cn1, toCn3 instead of 41741_1_1_1, 41742_1_1_3) for all plotting functions that are supplied...read.targets() to work like read.data, while the two functions may not know each other. row.namesa vector of row names. This can be a vector giving the actual row name…

Agi4x44PreProcess Agi4x44PreProcess

updated 16.7 years ago • Massimo Pinto

Given that `` vmatchPattern `` doesn't work with a vector as the pattern and `` vmatchPDict `` isn't implemented, are there alternatives in R that don't involve using short read mapping

Biostings Biostrings

updated 9.1 years ago • Dario Strbenac

div class="preformatted">Hi, I want to multiply a vector (1st argument) by another vector or a matrix (2nd argument) depends if a column or a row of a matrix or a subset of a matrix...is taken. The first argument presents a coefficient vector (of 1 or more elements) that will be multiplied by all elements of the 2nd argument. Therefore, the final product (multiplication...of the 2 arguments) w…

updated 16.8 years ago • carol white

s not what > base::unique() does, > (b) we choose to have unique() drop the names and metadata columns > of any Vector object (DNAStringSet, GRanges, etc...), > (c) we add the 'use.names' and 'use.mcols' args to...use cases are. Whatever we do, we should have unique() behave > consistently on any member of the Vector family and also treat &am…

Cancer Cancer

updated 13.0 years ago • Hervé Pagès

help(ShortRead:::.freqSequences) Error in help(ShortRead:::.freqSequences) : 'topic' should be a name, length-one character vector or reserved word > help(.freqSequences) No documentation for ?.freqSequences? in specified

updated 13.4 years ago • wang peter

number of genes=31099 annotation=rat2302 notes= > QCReport(affy.batch.sub) Error in attr(groups, "names") <- names : 'names' attribute [16] must be the same length as the vector [1] Enter a frame number, or 0 to exit 1: QCReport(affy.batch.sub...2: signalDist(object) 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = "Array 4: boxplot.default(object, names…

affy affy

updated 18.4 years ago • Mark W Kimpel

dataPath <- system.file(experimentName, package="cellHTS2") x <- readPlateList("Platelist.txt", name=experimentName, path=dataPath) x <- configure(x, descripFile="Description.txt", confFile="Plateconf.txt", logFile="Screenlog.txt...path=dataPath) negCtr <- vector("character", length=di…

updated 15.2 years ago • Ning

returns NULL with no warning or error message. I have tried changing the subject ids to character, or integer, or numeric, but I continue to get NULL. Without any error message to work with I am at a loss. Any advice? Should...the offspring, mother and father vectors be scan ids or scan/subject names? My scan names are not numbers and so these vectors would not satisfy the requirement...in t…

GWASTools GWASTools

updated 13.3 years ago • Samuel Younkin

According to the GenomicFeatures annotation and this [post][1] it was a conscious decision to not include gene_name in the TxDb objects from the GenomicFeatures package. Is the decision of not including gene names something that could be brought up again? I think we can all agree that in the end the majority of end users would like gene...in the TxDb objects from the GenomicFeatures packag…

Bioconductor GenomicFeatures TxDB

updated 5.1 years ago • k.vitting.seerup

with the pathway of interest (_i.e._ "autophagy induction") for yeast and human are provided in two named character vectors _“yeast.ai.proteins”  _and "_human.ai.proteins_”.  I found the detail for how one could do...packages/release/bioc/html/biomaRt.html) to get the other information and put it into a character vector like so: <pre> > head(human.ai.protein…

Path2PPI

updated 7.9 years ago • moldach

recipEdges = "distinct", layoutType = "dot", nodeAttrs = natt, name = "", edgeAttrs=list(c(color='green', weight=0.3) ) ) Error in buildEdgeList(graph, recipEdges, edgeAttrs, subGList, attrs$edge) : STRING_ELT...can only be applied to a 'character vector', not a 'NULL' He…

updated 17.9 years ago • Srinivas Iyyer

0 0 0 0 0   `` I cannot plot  a graph because my row names and column names dont match. `` library(graph) g = as(x4, "graphNEL") plot(g, "neato") Error in asMethod(object) : 'rownames(from)' and ' colnames...from)' must be identical

graph rgraphviz

updated 11.1 years ago • tyrone.williams.701

I find that unlisting the GenomicRanges returned from a call to `transcriptsBy` returns a list with names that are gene names... only they are incorrect! Look: > txdb<-makeTranscriptDbFromBiomart(biomart="ensembl", dataset...ranges strand | tx_id tx_name <rle> <iranges> <rle> | <integer> <character> [1] 2R [18024494, 18060339]…

GenomicRanges GenomicRanges

updated 13.3 years ago • Malcolm Cook

I am getting this error- "x must be numeric" when running this code. I am working on a pre processed data. The data frame is list. ``` #moderated t test using limma...file <- rma # Column 1 contains row-names group <- rep(0:1, c(3,5)) library (limma) lmFit(object, design=NULL, ndups=1, spacing=1, block=NULL, correlation, weights=NULL, method

limma

updated 4.0 years ago • keervanik

R 3.2.1(and 3.2.0), ath1121501.db 3.1.3, AnnotationDbi 1.30.1   This should return "Large character (20335 elements, 1.2 Mb)" You can reproduce the "Large character (20335 elements, 1.2 Mb)" with R 3.1.3, ath1121501.db 3.0.0

annotation arabidopsis thaliana

updated 10.5 years ago • knishida

ranges = IRanges(start = 1:2, end = 4:5)) ``` I want to change the chromosome names all to "chrX" ``` > seqnames(gr) <- "chrX" Error in .normalize_seqnames_replacement_value(value, x) : levels of supplied 'seqnames...must be identical to 'seqlevels(x)' ``` Please let me know if there is a simple way to do this. Best regards

genomicrang GenomicRanges

updated 4.2 years ago • changxu.fan

method = "glmLRT", + paired=FALSE) And it gives: "Errore in names(x) <- value : l'attributo 'names' [7] dev'essere della stessa lunghezza del vettore [1]" . I suppose that the two vectors "dataSmNT_short.miR

miRNAseq TCGAbiolinks TCGAAnalyze_DEA

updated 4.1 years ago • Gandino

lawremi/rtracklayer/issues/13) but in my hands it fails although I made sure my chromosome vector was of type character Any help would be very welcome as well as for attaching the FASTA genome sequence to this database...but then !** Seqinfo(gr) Error in .normargSeqlevels(seqnames) : supplied 'seqlevels' must be a character vector > str(chr.info) 'data.frame':…

GenomicFeatures rtracklayer

updated 6.7 years ago • stephane.plaisance

closely), but in the >> "Arguments" section, the mode argument is described as: >> "A character(1) vector; mode="rw" indicates a binary (BCF) ?le, >> mode="r" a text (VCF) ?le" >> when it should probably be >> "A character...1) vector; mode="rb" indicates a binary (BCF) ?le, >> mode="r" a text (VCF) ?le" >&…

VariantAnnotation Rsamtools VariantAnnotation VariantAnnotation Rsamtools VariantAnnotation

updated 14.3 years ago • Valerie Obenchain

different the differing results I get when I change a comparison variable in the design formula from character, to factor. i am comparing differential expression across age groups. The data has a variable 'age' : with these values...0.0230828518 0.17758857 -0.12997938 0.8965827428 0.96129754 but when I run it with 'age' as a character get : Gene baseMean log2FoldChange …

DESeq2

updated 22 months ago • James Aiden

Error in spia(de = DE\_Colorectal, all = ALL\_Colorectal, organism = "hsa",  :   de must be a vector of log2 fold changes. The names of de should be included in the refference array!   Could you please help! Regards

SPIA

updated 9.5 years ago • saamar.rajput

org.Hs.eg.db', details: call: match.arg(synchronous, c("off", "normal", "full")) error: 'arg' must be NULL or a character vector Error: package or namespace load failed for ‘org.Hs.eg.db’ > traceback() 2: stop(gettextf("package

annotationdbi annotation organismdb loadnamespace

updated 11.1 years ago • milorobertsmith