Bioconductor Forum

<div class="preformatted">Dear List, During GCRMA using simpleAffy package for some array data (>30) it is showing: "Error: cannot allocate vector of size 372.1 Mb" R environment is as follows: R version 3.0.1 (2013-05-16) -- "Good Sport" Copyright (C) 2013 The R Foundation for...GCRMA using simpleAffy package for some array data (>30) it is showing: "Error: cannot allocate…

gcrma simpleaffy gcrma simpleaffy

updated 12.5 years ago • chittabrata mal

Good morning, I saw this massage r: vector memory exhausted (limit reached?) In addition: Warning message: In fread(f, header = TRUE, sep = "\t", stringsAsFactors = FALSE...Good morning, I saw this massage r: vector memory exhausted (limit reached?) In addition: Warning message: In fread(f, header = TRUE, sep = "\t", stringsAsFactors = FALSE, : …

TCGAbiolinks Methylation GDC data Data prepare

updated 6.0 years ago • ph.shimaasherif

class(matureInspObj) # "INSPEcT_steadyNoNascent" tpts [1] "0mock" "60mock" # tpts is a character vector with the names of the different steady-state conditions corresponding to the columns in the totExp_plgem

INSPEcT

updated 2.9 years ago • MK

end) > targetTrack <- with(targets,GRangesForUCSCGenome("hg18", chrom, targetRanges, strand,name, target)) > session <- browserSession("UCSC") > track(session, "targets") <- targetTrack Fehler in genome(seqinfo(x)) : Fehler...f??r Funktion 'genome': Fehler in .normargSeqlengths(seqlengths, seqnames) : supplied 'seqlengths' must be a vector R version …

rtracklayer rtracklayer

updated 14.0 years ago • Guest User

fisher",verbose=F) Error in spia(de = WThypo, all = WThypo1, organism = "mmu", nB = 2000, : de must be a vector of log2 fold changes. The names of de should be included in the refference array! I am not sure what I did wrong

Organism SPIA Organism SPIA

updated 14.4 years ago • Jing Huang

Hi, I have tweaked the read.marrayRaw code so the scan function accepts a "what" list of mode character for the 5 odd columns of interest, and NULL for the 77 odd unwanted columns in a gpr file The change is to the following...h <- strsplit(readLines(f, n = skip + 1), split = sep) # h <- as.list(unlist(h[[length(h)]])) # names(h) <- gsub("\"", "", unlist(h)) replacing…

updated 22.5 years ago • Marcus Davy

included from integer\_matrix.cpp:1:0: integer\_matrix.h:21:9: error: ‘Rle\_lin\_matrix’ does not name a type integer\_matrix.cpp: In function ‘std::unique\_ptr<beachmat::lin\_matrix<int, Rcpp::Vector<13> > > beachmat..._ptr(std::unique\_ptr<\_Tp, \_Dp>&&) \[with \_Tp = beachmat::lin\_matrix<int, Rcpp::Vector<…

beachmat compilation error

updated 7.9 years ago • daniel.gaffney

in loadNamespace() for 'rJava', details:   call: dirname(this$RuntimeLib)   error: a character vector argument expected --------------------------------------------------------------------------------------------------------------------------------- Could you please help me to solve this issue? Thanks and best regards, Adham

BioMedR

updated 8.0 years ago • adham_star50

div class="preformatted">Hi, I am trying to replace a single numeric value in a matrix with a character vector. >mat[5580, 4] [1] 838.1 > mat.r <- replace(mat, mat[5580, 4], "NA") I don't get any errors. However when I go to see if the

GO GO

updated 13.3 years ago • Mark B

parasite.. I'm not sure how to proceed. I have been looking into e1071 package in R for support vector machine, but I'm not sure this will give me the right model. I am very grateful for any help / advice anyone can think of Thank

updated 17.1 years ago • Celine Carret

obvious help in archives. My protein sequences will be read in as fasta strings and converted to a character vector. x <- "MSETNKNAFQ" strsplit(x,"") I have the scores for the 20 amino acids (letters in column 2 of a table), and the scores...this "c(\"4.2\", \"-0.4\", \"-4.5\", \"4.5\")" which I can't work out how to convert to a usable vector. Once I have my numeric vector I want to ca…

graph convert graph convert

updated 21.1 years ago • Matthew Hannah

Hi, is there a way to convert a sequence (in my case a fastA character vector) into a IRanges object based on a numeric vector? the vector contains the positions of a specific pattern

iranges fasta split

updated 8.9 years ago • Assa Yeroslaviz

ENSMUST00000177564 ENSMUST00000196221 ... ENSMUST00000158369 ENSMUST00000183553 rowData names(9): tx_id tx_biotype ... gc_content tx_name colnames(10): SRR6868519 SRR6868520 ... SRR6868527 SRR6868528 colData names(8...ENSMUST00000174625 ENSMUST00000174382 ... ENSMUST00000175508 ENSMUST00000177296 rowData names(16): tx_id tx_biotype ... locfdr qvalue colnames…

fishpond swish

updated 5.6 years ago • 1911449

db.password) I keep getting this: SET_VECTOR_ELT() can only be applied to a 'list', not a 'character' Calls: dbConnect ... dbConnectionInfo -> dbConnectionInfo.PgSQL.conn -> .Call This used to work fine under R 2.7

RdbiPgSQL RdbiPgSQL

updated 16.7 years ago • Philip Lijnzaad

in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : In range 21: 'end' must be >= 'start' - 1

cn.mops

updated 3.3 years ago • User000

ALT QUAL FILTER <DNAStringSetList> <numeric> <character> 1:12783_G/A A 33.56 . 1:13110_G/A A 103.15 . 1:13116_T/G G 1681.37 . 1:13118_A/G G 1591.21 .</pre>     I would like to…

bioconductor

updated 8.7 years ago • Haiying.Kong

Error in buildXYData(table, status, main, display.columns, anno, counts, : Length of groups must be equal to the number of columns in counts. The R feedback was 4. stop("Length of groups must be equal to the number of columns

Glimma RNASeq

updated 4.0 years ago • Jonas

lt;-\`(\`\*tmp\*\`, value = c("seg.name", "seg.Start", "seg.End",  :     'names' attribute \[5\] must be the same length as the vector \[3\] I also tried changing the seg.name names:     n <- 17 &nbsp...seg.dat = par.chr, seg = seg.name)     > attributes(par.chr)  &…

r omiccircos

updated 8.9 years ago • theobroma22

Hello, I am running DESeq2 with this metadata table - | Condition | Time | Batch | |-----------|------|-------| | Control | 0h | 1 | | Control | 12h | 1 | | Control | 24h | 1 | | Control | 0h | 2 | | Control | 12h | 2 | | Control | 24h | 2 | | Control | 0h | 3 | | Control | 12h | 3 | | Control | 24h | 3 | | Control | 0h | 4 …

DESeq2

updated 13 months ago • bhandary.8590

comparable tissues lying around.  Is that enough to reliably generate new and usable frma vectors?   Thanks

annotation frma frmatools

updated 11.1 years ago • Tim Triche

names (gr) must fit). Could you please give me a hint. Thanks Hermann > df1 Strand A1 A2 rs3737728 u C T rs6687776 u C T rs9651273 u...seqnames ranges strand | score <rle> <iranges> <rle> | <character> rs3737728 chr1 [1021415, 1021415] * | 0.340955 rs6687776 chr1 [1030565, 1030565] …

updated 12.5 years ago • Hermann Norpois

lt;- decideTests(cont.matrix1) summary(cont.matrix1) volcanoplot(fit.cont,coef=1, highlight=50, names=seqdata$Transcript, main="ConeVsRoot", pch=10, cex=0.25) ``` My question is for one, how I can have the top 50 as a data frame so do...the sequences from the original assembly)? Also, I shortened the IDs and dropped the non-unique characters but still cannot have the whole name and it's not uniq…

limma edgeR Glimma

updated 3.0 years ago • Mohammad

<div class="preformatted">Hi, I am trying to analyze a set of flybase IDs with the DAVIDQuery package. I would like to make a clustering analysis of a list of genes, but I keep getting some error messages. I have a list of flybase IDs, eg. ids="FBgn0039239,FBgn0039337,FBgn0039350,FBgn0039356,FBgn0039494" With type type <- "FLYBASE_GENE_ID" tool <- "gene2gene" When I…

Clustering affy Clustering affy

updated 11.9 years ago • Assa Yeroslaviz

C2") msig_gsea_format <- function(gs){ #Get msig gene-sets into gsameth-format (-> list of character-vectors) #gs (data.frame): Object returned by msigdbr() #ls_gs (list): list of gene-sets consiting of character vectors...gs_name,entrez_gene) %>% tidytable::group_split.(gs_name, .keep = FALSE, .named = TRUE) ls_gs <- lapply(ls_gs, funct…

missMethyl GSEA minfi methylGSA

updated 3.0 years ago • Lukas

and 2 samples.] << Prepare Data Over. >> Error in cmdscale(d) : 'k' must be in {1, 2, .. n - 1} The complete code is as follows： pd10 <- data.frame(stringsAsFactors = FALSE, Sample_Name = c("GSM1669564","GSM1669589

MethylationArrayData

updated 3.2 years ago • shuangshuang

base content as well as pair of bases content. im using the following sniped of code: ###pmseq is a vector of character strings (not of the same nchar). tmp <- sapply(pmseq,function(x){ y = DNAString(x) c(alphabetFrequency(y)[2:5], ##count

Biostrings Biostrings

updated 19.9 years ago • Rafael A. Irizarry

to this method? The following is the partial scripts about positive controls posControls <- vector("character", length=dim(Data(x))[3]) posControls[1] <- list(act="(?i)^ntc2pluslps$", inh="(?i)^myd88$|^tlr4$|^irak1and4$") posControls[2] <- list

updated 15.2 years ago • Ning

I get two different objects of different classes incompatible with each other (I can't build a vector to go futher in the analysis).  VCF are output of Mutect2 pipeline.  Here is an example of the code I use:  <pre...and so the dimensions of the matrix), respectively 50x114 and 167x114.  When I try to make a vector : <pre> vr_HNCtot = c(vr_HNC2, …

somaticsignatures vranges readvcfasvranges

updated 7.3 years ago • guillaume.dachy

hi all, a rookie tilingArray question. i'm having trouble creating the perfect match index vector. for my probe set (n= 6490), each probe is a unique, perfect match to its target. i have created a probe index file that contains...vac_hyb_set, pm= pm_vector, background= bg_vector, cutoffQuantile= 0) this gives me an error: 'pm' must be an integer vector with values between 1 and 6490. any idea …

probe tilingArray probe tilingArray

updated 17.2 years ago • Anjan Purkayastha

mart = mart, : 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::getSequence...mart = mart, : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this on the support…

biomaRt

updated 5.9 years ago • tabbott

the examples but these use data that I'm not interested in. To use my own data for chromosome names and lengths and for gene names, positions and strands I gather I need to instantiate a chromLocation object. When I try...a Y axis. Please tell me where I'm going wrong! Thanks, Matthew library(geneplotter) # make a named vector of chromosome lengths: chromLengths <- c(10000,5000) nam…

geneplotter geneplotter

updated 22.6 years ago • Matthew Hobbs

div class="preformatted">I have a character vector of approximately 25000 genomic regions I want to retrieve additional genomic information for using biomaRt...attribs, mart=mart) The above query seems to run forever (3 days +), but when splitting the regions vector in two halves each is finished after approximately 15 minutes. Am I doing something wrong or is there an upper limit

biomaRt biomaRt

updated 15.4 years ago • Christian Ruckert

ranges strand | exon_id exon_name > <rle> <iranges> <rle> | <integer> <character> > [1] chr9 [21967751, 21968241] - | 127318 <na> > [2] chr9 [21968574, 21968770] - | 127319 <na> > [3] chr9 [21970901, 21971207] - | 127320...for insight into working with the…

Coverage Cancer IRanges GenomicRanges Coverage Cancer IRanges GenomicRanges

updated 12.8 years ago • Martin Morgan

variables or interaction terms in the design formula are linear combinations of the others and must be removed. Please read the vignette section 'Model matrix not full rank': vignette('DESeq2') In addition: Warning message...In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors &am…

DESeq2 BatchEffect DifferentialExpression

updated 2.7 years ago • AZ

gt;>> > loc2rsid(mylocs) >>> CharacterList of length 6 >>> [[1]] character(0) >>> [[2]] rs75258394 rs78180314 >>> [[3]] character(0) >>> [[4]] character(0) >>> [[5]] rs76676778 >>> [[6]] rs6518357...gt;&…

SNP Cancer SNPlocs ASSIGN SNP Cancer SNPlocs ASSIGN

updated 12.6 years ago • Fabrice Tourre

SR19_AA24_18Aligned.sortedByCoord.out.bam", isPaired = TRUE, name="S24", col="sandybrown", fill="sandybrown", cex=0.8) >for (i in 12:length(targets)){ ID<-targets[i] start<-genemodel$start[genemodel...feature=="CDS",], chromosome = chr, start = start, end = end, Id = ID, feature=ID, group = ID, …

Gviz plotTracks

updated 5.8 years ago • syliang

full.names=TRUE) Data <- read.celfiles(celFiles) I got this error: All the CEL files must be of the same type. Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE All CEL files are hg-1.1-st-Array

updated 12.2 years ago • Jerry Cholo

All, When I used ReadAffy() to read cel files about 8GB, it return a error: Error: cannot allocate vector of size 2.8 Gb How I can do with it? Thanks -- Best, Changhe Fu [[alternative HTML version deleted]] </div

updated 15.2 years ago • Changhe Fu

to *exclude* tags using `Rsamtools`, since the help for `ScanBamParam` says: ```tagFilter A named list of atomic vectors. The name of each list element is the tag name (two-letter code), and the corresponding atomic vector...reads with specified tags are included. NULLs, NAs, and empty strings are not allowed in the atomic vectors.``` Of course I can count the reads on the command line u…

rsamtools

updated 6.6 years ago • liz.ingsimmons

but the problem is still unsolved. I'm trying to run some R code and it is crashing because of long vector error. I'm running R 3.5.1 on Ubuntu 18.04.1 LTS and getting the following error: "Error in for (n in 1:k) { : long vectors not supported

r

updated 6.9 years ago • r.tor

x[[i]], optional = TRUE) : can't coerce marrayNorm into a data.frame etc sink gives -> file' must be NULL, a connection or a character string Any ideas the easiest way to retrieve data from marryNorm ? Thanks Jason </div

updated 22.9 years ago • Jason Skelton

connection made, file length 189222 bytes > opened URL > downloaded 184 Kb > > Error in names(x) <- value : > 'names' attribute [47] must be the same length as the vector [1] > In addition: Warning message: > closing unused

GEOquery GEOquery

updated 15.2 years ago • Sean Davis

read.table("samples.txt", header = TRUE) files <- file.path("quant", samples$sample, "quant.sf") names(files) <- paste0(samples$sample) txi.salmon <- tximport(files, type = "salmon", tx2gene = tx2gene)` I have successfully created...below: head(tx2gene) DataFrame with 6 rows and 2 columns tx_id gene_id <character> <charact…

Salmon tximport tximportdata ensembl

updated 5.7 years ago • slouis

columns title geo_accession organism age sex infection <character> <character> <character> <character> <character> <character> GSM2545337 CNS_RNA-seq_11C GSM2545337 Mus musculus 8 weeks...NonInfected strain time tissue mouse Label Group …

SummarizedExperiment

updated 15 months ago • Shuo GG

pathways for Drosophila and not C Elegans. For C Elegans you should use the sce instead of dme. The names of CH and the vector CH1 must be valid ENTREZ IDs for the respective organism. Adi Tarca [[alternative HTML version deleted

Pathways Organism SPIA Pathways Organism SPIA

updated 14.3 years ago • Tarca, Adi

this platform is different enough from ordinary HG-U133 arrays, that I'm not sure if the frma vectors would still apply, and if so, how one would apply them. (Specifically, the mismatch probes are removed, and some probesets...of 16 or 24 arrays, which could affect how one defines "batches". So my question is: Are there frma vectors available for this platform; or, can I obtain them easily by su…

frma frmatools

updated 10.9 years ago • Ryan C. Thompson

Read a file containing Entrez IDs and TAIR IDs. - Subset the Entrez IDs and converted to character vector. - Used the vector as genelist. -Used goProfiles package function basicProfile for this genelist with organism

goProfiles goProfiles

updated 12.4 years ago • Guest User

not equal to array extent The rd1 and rd2 objects are RangedData created using IRanges but the row names seem to be causing a problem. > dimnames(rd1) [[1]] NULL [[2]] [1] "site" "score" Compare this to the vignette example: > dimnames(peaks1...2 value columns across 16 spaces space ranges | peak strand <character> …

IRanges IRanges

updated 15.6 years ago • Noah Dowell

to do some plots but could not import hg19 reference genome fasta file. The error is  long vectors not supported yet: ../../src/include/Rinlinedfuns.h:137 Any idea how to increase the vector length so that big fasta can

vcf

updated 9.1 years ago • jenniewoo

affy.object,file=paste(experiment.designator, "AffyQCReport.pdf", sep=".")) Error in attr(groups, "names") <- names : 'names' attribute [29] must be the same length as the vector [1] Enter a frame number, or 0 to exit 1: QCReport(object = affy.object...paste(experiment.designator, "AffyQCReport.pdf", sep = ".")) 2: signalDist(object) 3: boxplot(object, names = ArrayIndex, ylab = "Log2(In…

cdf annotate affy limma RBGL simpleaffy GOstats affyQCReport cdf annotate affy limma

updated 18.9 years ago • Mark W Kimpel

Error in stop("need data package: ", annlib) : object "annlib" not found Error in get(paste(lib, name, sep = ""), mode = "environment"): variable "hugene10stv1ENTREZID" of mode "environment" was not found Error in get(paste(lib, name, sep...was not found Error in dim(data) <- dim : attempt to set an attribute on NULL Error in names(x)<-value : 'names' attribute[3] must be same l…

oneChannelGUI oneChannelGUI

updated 17.6 years ago • Steve Taylor

to have the strand information of the probes used, but I can't see what the required format of the names of the vectors is. Can anyone provide a small example of how it's done ? It would be nice if there was a simple way to do this...or GRanges object of probe information, rather than having having to create lots of specially named vectors and mess around with environments. Also, the chr argument…

updated 13.6 years ago • Dario Strbenac

tbi", sep=".")) vcf.rng <- readVcf(tab, "hg19", param=GRObject) Error: scanVcf: 'filename' must be character(1)</pre> As \`vcf.fl\` is a list of files instead of 1 file as in the introduction, I attempted to use \`TabixFileList...unable to find an inherited method for function ‘readVcf’ for signature ‘"TabixFileList", "character", "GRanges"’</pre> Clearly I am misunders…

variantannotation

updated 9.4 years ago • Kipper Fletez-Brant

<div class="preformatted">Hi, I am currently trying to use the SPIA bioconductor package and I came across an error that I am not sure how to solve it. I used the contrast.fit method from Limma to obtain a list of significantly differentially expressed genes. Following that, I wanted to use the SPIA package, but it kept on giving me the error : "Error in spia(de = DE_top, all = ALL_top, or…

Organism limma SPIA Organism limma SPIA

updated 15.6 years ago • Barbara Bo-Ju Shih

filtering bam file: RE: MEDIPS.createSet error And yes, the argument BSgenome is supposed to be a character string naming the BSgenome object. Please let me know, if this will work for you. Lukas P.S. I like the chr.select=seqnames...I do this, the literal BSgenome.Ptrichocarpa.Phytozome.v3 is assigned to the BSgenome variable as a character vector. So instead, I do this: BSgenome = BSgenome.Pt…

Alignment GO Cancer BSgenome BSgenome Rsamtools genomes MEDIPS Alignment GO Cancer

updated 11.8 years ago • Vining, Kelly

update2MIAME" [61] "varLabels" "write.exprs" showClass("exprSet") Slots: Name: exprs se.exprs phenoData description Class: exprMatrix exprMatrix phenoData characterORMIAME Name: annotation...notes Class: character character > showClass("MIAME") Slots: Name: name lab contact …

Annotation GO Preprocessing Biobase affy affyPLM Annotation GO Preprocessing Biobase

updated 21.8 years ago • Debjani Bhowmick

the following error: > updateCelUnits(pathname, cdf=NULL, intens) Error in dirname(filename) : a character vector argument expected > is.character(pathname) [1] TRUE > is.vector(pathname) [1] TRUE Since I do appear to be giving...it a character vector, I'm stumped. Can someone help? My session info appears below. Thank you very much! Mikki Behnke Doctoral Student

Microarray hgu133a2 affxparser Microarray hgu133a2 affxparser

updated 14.5 years ago • Martha Behnke

array=1, chrom.to.plot=8, chrominfo=1000) fails. Error in attr(status, status.attr[ii]) : 'which' must be of mode character I can remove the status lines from the code but I am still getting an error on chrominfo What is expected

updated 15.7 years ago • Chris Fenton

err msg: Error in read.table(file = file, header = header, sep = sep, quote = quote, : 'file' must be a character string or connection Any one has any clue on this? Thanks a lot! -Jack [[alternative HTML version deleted]] </div

PROcess PROcess

updated 11.8 years ago • Jack Luo

image). The upregulated genes are just greyed out. Data is a csv file with two columns: gene name in KEGG format, then log2fold change values in the second column. Code is below.![enter image description here][1] ```r > data...pathview_input_AN_OX.csv", header=FALSE) > geneList = data[,2] #importing fold change data as a vector > names(geneList) = as.character(…

pathview Proteomics

updated 10 months ago • Jessica