Bioconductor Forum

Hello. I have been struggling on finding a non-additive effect of combined two drugs. So, I have a dataframe defining treatment of my samples as follows: ``` # Define experimental conditions for each sample condition <- factor(c(rep("A",3),rep("B",3),rep("C",3),rep("D",3),rep("E",3))) batch <- factor(rep(1:3,5)) coldata <- data.frame(row.names=colnames(countdata),conditi…

DESeq2

updated 4.5 years ago • TJ

the commands I used: > > conditions = c( "HCV1", "HCV1", "HCV1", "HCM1", "HCM1", "HCM1" ) > names(conditions) <- c( "accepted_hits_ATCACG.sorted.bam", "accepted_hits_CGATGT.sorted.bam", "accepted_hits_TTAGGC.sorted.bam...I got an error: > Error in match.arg(trend, c("none", "movingave", "tricube")) : > 'arg' must be NULL or a character vector > &…

Organism edgeR easyRNASeq Organism edgeR easyRNASeq

updated 13.1 years ago • delhomme@embl.de

name must be a character vector. The current input is ", class(files))) } } else { if (is.na(files) || is.null(files)) { stop(paste0("Error: the argument...else { stop(paste0("Error: the argument to '", opt, "' must be a character vector. The current input is ", class(file…

Rsubread featurecounts coercion

updated 4.3 years ago • Konstantinos Yeles

div class="preformatted">An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20071126/ 1d89aece/attachment.pl</div

updated 17.8 years ago • Ingrid H. G. Østensen

objects. See ?unstrsplit Cheers, H. On 12/16/2013 06:51 PM, Michael Lawrence wrote: > Btw, the name strunsplit is way better than my pasteCollapse. Maybe > tweak it to unstrsplit? Feels more like a verb. > > > > On Mon...XStringSetList("__B", x) > if (!isSingleString(sep)) > stop("'sep' must be a single character str…

Annotation Cancer Biostrings IRanges Annotation Cancer Biostrings IRanges

updated 11.8 years ago • Hervé Pagès

using? > >If db is the character vector with the annotation database for your array > >without the .db extension, then what does db represent? &gt...NA))) > >> l[[i]] = genelist[is.element(genelist,kegg[,1])] > >> } > >> names(l)=KEGGID > >> l > >> } > …

Annotation Pathways GO rat2302 probe affy Category Annotation Pathways GO rat2302 probe

updated 14.9 years ago • Mike Walter

to re-run a couple of new comparisons using DESeq2. I have previously used this script but something must have changed or updated in the last couple months that is responsible for this. I am trying to perform differential gene...technical replicates coldata=as.data.frame(cbind(location, temp, individuals)) row.names(coldata) = names(countData) coldata # ----------Construct data object ---------…

DESeq2

updated 4.8 years ago • Amy

in my script the following informations: 1. list with fields R, G, Rb and Gb giving the column names to be used for red and green foreground and background; 2. character vector of names of other columns to be read containing...spot-specific information; 3. character vector of names of columns containing annotation information about the probes; Is there someone that can answer

limma limma

updated 16.8 years ago • Giusy Della Gatta

and with different kinds of sequences (amino acid) and received the same error message -- I'm sure I must be missing something. My R output is below. Thanks so much for any help! -- output of sessionInfo(): > genes<-keggLink("ath00906...genes[1:10,2],"ntseq") > head(sequences) A DNAStringSet instance of length 6 width seq names [1] 17…

PROcess KEGGREST PROcess KEGGREST

updated 12.0 years ago • Guest User

<div class="preformatted">I have two data frames with a name column containing affy probeset ids. I would like to pull out the ids (just the ids) which are common in both data frames. (Actually...div class="preformatted">I have two data frames with a name column containing affy probeset ids. I would like to pull out the ids (just the ids) which are common in both data frames...I could ju…

affy ASSIGN affy ASSIGN

updated 21.4 years ago • Straubhaar, Juerg

general R question, not specifically BioC, but I imagine is something that the "bio" people here must have encountered at some point. I would like to include the symbols for male and female in a legend for a plot. How do I obtain...that? Is there a function that will show me all the characters available in the font that R is using? I have been looking in the manual etc but I haven't found what …

updated 18.7 years ago • J.delasHeras@ed.ac.uk

a XML document but I have a problem to use URI to retrieve that file, since URI can also contain characters, which should not be there according to http://www.faqs.org/rfcs/rfc2396.html I encountered problems with "[" and...as well as with space characters. However there might also be a problem with others i.e. reserved characters in URI syntax. My R example is: R> library...1] "1.0" …

updated 20.4 years ago • Gorjanc Gregor

Hi folks, I have a set of short DNA sequences containing the R character (for A or G). I used readDNAStringSet to convert my fasta input file to a DNAStringSet, then the Disambiguate function...analysis, keeping the original identifiers, appended with a number/letter, to give a unique name to each disambiguated sequence. I have been playing with DECIPHER's DB2Seqs function, but I don't seem to un…

DECIPHER FASTA disambiguate

updated 5.3 years ago • joannew

gt; hg19_tx <- extractTranscriptsFromGenome(Hsapiens, hg19txdb) #Create DNAStringSet with names associated with each probe > probeset <- DNAStringSet(probelist$sequence) > names(probeset)<-probelist$probenames...probes in ps_pdict to transcript 14 in hg19 and gives: >unlist(txmatches): start end width names [1] 749 773 25 HW:6 [2…

probe probe

updated 14.1 years ago • Ian Henry

correction on filtered data from genepix files. I've read my genepix data into and RGList (cleverly named RG) via a wt.fun function that filters out certain control spots that I don't want thrown into the analysis. In other words...data set and run kooperberg on it. The problem I'm having is that Kooperberg apparently requires a character vector containing genepix filenames as its initial argumen…

updated 20.0 years ago • scholz@Ag.arizona.edu

<div class="preformatted">hi all -- does anyone know how to turn off the forced conversion of character vectors to factors when merging with IRanges::DataFrame objects? in the example below fooX.df is a base data.frame, while fooX.DF is the IRanges::DataFrame equivalent. example: > foo1.df <- data.frame(a = letters[1:10], b = runif(10), stringsAsFactors = FALSE); foo1.DF &am…

updated 12.1 years ago • Murat Tasan

<div class="preformatted">Hello everyone, Could somebody show how to convert ShortReadQ qualities to characters? A little detail: For instance, I can load into memory a ShortReadQ instance, A <- readFastq('file.fq.gz') and then I...div class="preformatted">Hello everyone, Could somebody show how to convert ShortReadQ qualities to characters? A little detail: For instance, …

convert convert

updated 11.2 years ago • Ivan Gregoretti

ENSG00000000005 ... ENSG00000273492 ENSG00000273493 rowData names(9): gene hgncl ... colnames(100): 1 1 ... 99 100 colData names(13): ID SAMPLE I have tried: data_matrix <- data@assays[[1]] data_filtered...data_matrix))>1,] but got an error: Error in count(data_matrix) : Argument 'x' must be a vector…

summarizedExperiment

updated 5.9 years ago • annkolman78

details:   call: match.arg(synchronous, c("off", "normal", "full"))   error: 'arg' must be NULL or a character vector Error: loading failed Execution halted ERROR: loading failed \* removing ‘/home/warren/R/i686

software error org.hs.eg.db

updated 10.8 years ago • warren.anderson

But I am havig the following message: Error in heatmap.2(mat2, ...) :    'ColSideColors' must be a character vector of length ncol(x)   I understand the concept but I do not know how to fix it. Thanks! PJ &nbsp

heatmap

updated 10.3 years ago • PJ

dev <- computeDeviations(object = rse, annotations = motif_mm) ``` ``` Error in names(res) <- nms : 'names' attribute [386] must be the same length as the vector [302] In addition: Warning message: stop worker failed...dim: 4446140 386 metadata(0): assays(1): motifMatches rownames: NULL rowData names(2): name bias colnames(386): MA0025.1_NFIL3 MA0030.1_FOXF2 ... MA090…

chromVAR computeDeviations

updated 5.2 years ago • mkarimzadeh

Error in makeContrasts(MT_3hvsMT_0h = (M_A3h + M_D3h + M_G3h + M_K3h - : Parameter names must by syntactically valid names in R But my same command had worked on a reduced dataset just a few days earlier. Turns...in makeContrasts(MT_3hvsMT_0h = (M_A3h + M_D3h + M_G3h + M_K3h - : Parameter names must by syntactically valid names in R > colnames…

limma limma

updated 17.5 years ago • Yannick Wurm

I'd like to subset the matrix of expression values (exprs(lumi.batch.object) by probe ID, i.e. row names. Is there an obvious (and quick) sub-setting method to do that? If I use plotSampleRelation I can choose a selection of probes...selProbe parameter) but I guess it has to be as numeric vector, am I correct? In fact I tried to put the character vector containing probeID/row names and it didn't…

probe probe

updated 16.8 years ago • Emanuele Marchi

I'd like to subset the matrix of expression values (exprs(lumi.batch.object) by probe ID, i.e. row names. Is there an obvious (and quick) sub-setting method to do that? If I use plotSampleRelation I can choose a selection of probes...selProbe parameter) but I guess it has to be as numeric vector, am I correct? In fact I tried to put the character vector containing probeID/row names and it didn't…

probe probe

updated 16.8 years ago • Emanuele Marchi

probes,mouse4302SYMBOL,ifnotfound=NA) > Error in .checkKeysAreWellFormed(keys) : > keys must be supplied in a character vector with no NAs -- Sent via the guest posting facility at bioconductor.org. </div

updated 12.9 years ago • Guest User

Hi all, I am trying to compile the updated genome of the model plant Arabidopsis thaliana, from TAIR10. I am using the function forgeBSgenomeDataPkgFromNCBI but I am running to the error that the data contains ambiguity characters in sequences. I used Biostrings::replaceAmbiguities() but I am not sure how to save the updated version and I don't...function forgeBSgenomeDataPkgFromNCBI but I a…

BSgenomeForge

updated 2.0 years ago • Bruno

I was wondering if there is a way of specifying an argument to readDNAStringSet to ignore non-DNA characters? I have a set of .fasta files from IMGT that include their preferred gap notation, i.e. sequences that have some DNA...as.character() |> str_remove(pattern = "\\.") |> DNAStringSet() |> `names<-`(names(sequence1)) ``` Feels rather…

Biostrings

updated 1 day ago • biomiha

NAs should preferably be removed. How to best do this? the `` select() `` function only accepts a character vector... (as expected).   <pre> > library(org.Hs.eg.db) > myGenes[1:3,1:15] V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15...c("SYMBOL"),keytype="ENTREZID") Error in .testForValidKeys(x, keys, keytype, fks) : 'keys' must…

annotation

updated 8.7 years ago • Guido Hooiveld

command. The problem is, when I only have one file, there is an increment 1\_ in front of my custom name. I print both the length of d and my new custom name and they have the same length (1). From what I have read in the write.flowSet...page,  <span style="background-color:Yellow">Alternatively, one can supply either a character scalar, in which case the prefix `` i_ ``…

flowcore write.flowset()

updated 8.6 years ago • jordan.xanthopoulos

the new "combined" affybatch object as expected, however there are problems with the gene and sample names. geneNames(AffyBatch) returns a list of names from the new "combined" object, however when I extract the expression matrix...from the AffyBatch object(using exprs(AffyBatch)), the matrix has no gene or sample names associated with it (no row or column names. sampleNames(AffyBatch) returns …

cdf matchprobes cdf matchprobes

updated 21.7 years ago • david neil hayes

8 7 9 7 8 244973 4 3 2 6 7 244973 8 5 3 6 8 I would like to extract only the probe names and tried this: degtl - original matrix( containing 22810 entries) ids <- degtl[,1] and I got head(ids) [1] 244941_at 244959_s_at...244905_at 244906_at 244907_at 244908_at ... AFFX-TrpnX-M_at. I would like to extract the probe names as a vector in the following form : ids<-…

probe probe

updated 12.9 years ago • Guest User

gt; txdb= makeTxDbFromUCSC(genome= "hg19", tablename="ensGene") Error in names(trackIds) <- sub("^ ", "", sapply(nodes, xmlValue)) :   'names' attribute \[211\] must be the same length as the vector \[209\] any ideas how

genomicfeatures

updated 7.8 years ago • arko.sen1

keytype="ENTREZID") ``` Error in .testForValidKeys(x, keys, keytype, fks) : 'keys' must be a character vector The input of column row is ENSMUSG***** gmt pathway is mh.all.v2024.1.Mm.symbols.gmt Any suggestions

gsea mice org.Mm.eg.db

updated 10 months ago • Gordon

DataFrame with 1 row and 4 columns query X_id civic._license <character> <character> <character> 1 chr1:g.115258745C>G chr1:g.115258745C>G https://goo.gl/gPCAyH …

annotation software error myvariant

updated 6.7 years ago • Icke Blanco

I'm submitting a large query to Biomart, using the R package. The batch query was processing, made it about 38% of the way before throwing an error, which included "Please report this on the support site at http://support.bioconductor.org" the full error message is here: "Error in getBM(attributes = c("entrezgene_accession"), filters = c("external_gene_name"), : The query to the BioMart …

biomart R

updated 6.2 years ago • benjaminbarnhart19

<div class="preformatted">Hi Nico, Sorry it's taken awhile to get back to you. I wanted to ask about what behavior you'd expect from a call to unique() on a DNAStringSet, i.e., what is your use case? unique() on a named character vector drops names: chr <- c(a="A", c="C", aa="A", c="CC") > unique(chr) [1] "A" "C" "CC" Same for a named list: lst <- list(a="A", c="C…

updated 12.8 years ago • Valerie Obenchain

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 Here is my code: ensembl...counts_table_annotated$`Ensembl ID`, mart = ensembl) counts_table_annotated$Ensembl ID is a character vector of Ensembl IDs. Any help with this error would be appreci…

biomaRt

updated 6.2 years ago • Lucy

samples <- list.files(path = "./data", full.names = T, pattern="salmon$") ## Obtain a vector of all filenames including the path files <- file.path(samples, "quant.sf") ## Since all quant files have the same name it...is useful to have names for each element names(files) <- str_replace(samples, "./data/", "") %>% str_replace(".salmon",…

deseq2

updated 5.0 years ago • liqinrobin08

error:  Error in .normargGenome(value, seqnames(x)) :    supplied 'genome' must be a vector or factor  These were the steps I was running: library(Gviz) library(GenomicRanges) library(GenomicFeatures...txdb <- makeTxDbFromGFF("/home/m.tub1.gff3",circ\_seqs=character(), organism="Mycobacterium tuberculosis") annoData <- genes(tx…

Gviz plot chipseq

updated 8.0 years ago • anupriyaverma1408

error: Please help. TIA 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Error in names(x) <- value : 'names' attribute [2] must be the same length as the vector [1] Calls: tximport ... summarizeToGene -> .local -> cleanTx2Gene

salmon tximport

updated 3.6 years ago • Pragathi

I want to change the  labels of observations on the plot, which is defaulted as the row name of m data set.  But, I do not know how to define the labels ("indices of "x") that I want to display in my PCA plot.  following...the argument in the manual:  "parLabVc,   Optional character vector for the labels of observations on the plot…

R ropls

updated 7.3 years ago • yuan.guo001

Hi,  I tried use DESeq2's __PlotMA function__ and got the following error message -  <pre> <span style="background-color:Yellow">> plotMA(resKD_fc1) </span>Error in as.vector(data): no method for coercing this S4 class to a vector</pre> How do i resolve this issue? And what does it mean?      The__ sessionInfo__ i…

deseq2

updated 10.4 years ago • Jessica Chen

se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: character I check my count matrix and I don't see any character specified only numeric values except row names as genes and...colum names as samples. Then I also run the script to see if my count matric is numeric all(is.numeric(cts)) False I don't know where creating

deseq2

updated 5.3 years ago • imran khan

div class="preformatted"> Hi, I have a situation where I have a vector of variable names. If I call any of them, I get a text string (the name is surrounded by ""). How can I use that as a variable name...again? For instance, I have objects a, b and c, and a vector v<-c("a","b","c"). If I want to return the contents of a, I can't do just v[1], because that only shows "a"... Is there a…

updated 18.6 years ago • J.delasHeras@ed.ac.uk

Hello all, I am trying to analyze a plant metabolomics database with PAPi, but haven't been able to get even started as there is a constant error apparently related with the data formatting. All examples from the package work fine, and my own data looks in the same format as the example metabolomics data set. My database contains 20 compounds (rows) and 80 samples (columns), the column names are…

papi metabolomics pathway analysis

updated 8.6 years ago • hp71727

div class="preformatted">An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20050901/ c6ab8d9e/attachment.pl</div

updated 20.1 years ago • Groot, Philip de

gt; colnames( counts ) <- paste(c(rep("Gene.ID",1),rep("Reads.Count",1)),sep=",") \# sample names Error in \`colnames<-\`(\`\*tmp\*\`, value = c("Gene.ID", "Reads.Count")) :    'names' attribute \[2\] must be the same length as the vector

software error edger columns

updated 9.3 years ago • t3h096

the R documentation i perfectely obtaine the enrichment. >data(pho_sites_count) >genes<-names(rev(sort(pho_sites_count[,1]))[1:300]) > summary(genes) Length Class Mode 300 character character > is.vector(genes) [1] TRUE...lt;-find_enriched_pathway(genes,specis='hsa') However, when I use my datasets, which I submit as character vector with NCB…

KEGGprofile

updated 11.0 years ago • artur

in validObject(.Object) : invalid class “SummarizedExperiment” object: 1: invalid object for slot "NAMES" in class "SummarizedExperiment": got class "array", should be or extend class "character_OR_NULL" invalid class “SummarizedExperiment...object: 2: 'names(x)' must be NULL or a character vector with no attributes</pre> The same error occurs if you just take counts: <pre> c…

deseq2 tximport

updated 8.0 years ago • ben

div class="preformatted">I notice that edges appear to be named in two different ways: > edgeNames (g) [1:2] [1] "1~2" "1~3" > names (edgeData (g)) [1:2] [1] "1|2" "1|3" Does this different choice for separator character

updated 14.7 years ago • Paul Shannon

The goal is to obtain differentially expressed genes at low pH shared by all three cell lines. names cell pH Sample1 MDA low Sample2 MDA low Sample3 MDA low Sample4 MDA normal Sample5 MDA normal Sample6 MDA normal Sample7...function duplicateCorrelation…

limma

updated 5.3 years ago • gulusunshine

GenomicAlignments) <code>txdb <- makeTxDbFromGFF(refgff3, format = "gff3", circ_seqs = character()) #or gtf ebg <- exonsBy(txdb, by="gene") bamfile <- BamFile(readsBAM) se <- summarizeOverlaps(features=ebg, reads=bamfile...Error in .normargSeqlevels(seqnames) : supplied 'seqlevels' cannot contain duplicated sequence names</pre> …

software error

updated 7.5 years ago • c.legrand

which appear green, red and yellow in the plot nAttrs$label <- nodesNames nAttrs$height <-"3" names(nAttrs$height) <- "height" nAttrs$fontsize <- "20" names(nAttrs$fontsize) <- "fontsize" plot(mapkG, "dot", nodeAttrs=nAttrs) I tried...Doing this an error message ('Error in buildNodeList(graph, nodeAttrs, subGList, attrs$node) : the character vector must have…

KEGGgraph KEGGgraph

updated 14.8 years ago • Unger, Kristian

paste(LETTERS, collapse = '')) DataFrame with 1 row and 1 column test <character> 1 ABCDEFGHIJKLMNOPQRST.. ``?`show,DataFrame-method` `` seems not.</character

S4Vectors

updated 10 months ago • Dario Strbenac

specific person you hope will answer. At 04:49 PM 2/8/2010, you wrote: >Hi Dr Drnevich, >My name is Anatole and I work at UCLA. I found your code for >removing probes and probesets from affy on Bioconductor help website...pre-processing and normalization. You don't need to use RemoveProbes to filter - you can just use a character vector of the probe set names to subset your …

Normalization cdf probe affy Normalization cdf probe affy

updated 15.6 years ago • Jenny Drnevich

to load in the preinstalled data but when i try my own i get the error Error in split.default(names(sort(nl)), f.index): first argument must be a vector I have found some similar post/problems but i still cannot identify the...extract the adjusted p-values from our results object geneList <- res$padj # add the gene names from our results to our list of adjusted p-values names(…

topGO GO

updated 2.7 years ago • peter

1.38.3 >hg19db <- makeTxDbFromUCSC(genome = "hg19",tablename ="knownGene") Error in names(trackIds) <- sub("^ ", "", nms[nms != "new"]) : 'names' attribute [212] must be the same length as the vector [211] </pre>   Does anybody have the

maketxdbpackagefromucsc rtracklayer genomicfeatures

updated 7.2 years ago • lalchungnungabt17

file and would like to extract gene expression for further analysis. However, there is no name for the assay, how I can change the name or subset data. Thank you data class: SummarizedExperiment dim: 15093 100 metadata...rownames(15093): ENSG00000000003 ENSG00000000419 ... ENSG00000273488 ENSG00000273489 rowData names(3): Ensembl_ID GeneID EntrezID colnames(10…

deseq2

updated 5.2 years ago • georgina.fqw

Placebo.1h-Placebo.0h). Reading the DESeq2 manual I can use contrast using a list of two character vectors or a numeric contrast vector. Both requires to use the names in resultsNames but in resultsNames I do not...get all the names that I need. Is there a way to obtain DrugvsPlacebo.1h = (Drug.1h-Drug.0h)-(Placebo.1h-Placebo.0h) using all the experimental

deseq2

updated 5.4 years ago • ribioinfo

Hi, I am trying to use annotatr with custom annotations from a bed file to annotate differentially methylated regions. the bed has the following columns: chr, start, end, name (enst), score, strand, enst, entrez_ID, gene_name. I have tried a couple of options but did not manage to have the enst, entrez_ID, gene_name in the annotations. Below are my attempts and corresponding errors. Any advi…

annotatr

updated 2.4 years ago • luca.s