Bioconductor Forum

inputFilePath, format = "fasta", findgRNAs = TRUE,  :    Please enter a name for the gRNA ouput file name! Could you please advise as to how I name the gRNA output file as I am unable to do this. Thanks

CRISPRseek OutputFileName

updated 9.2 years ago • bhanson1806

VCF requires unique row names, but the formula used to generate placeholder row names can produce duplicates (Such as for pindel with default parameters...VCF requires unique row names, but the formula used to generate placeholder row names can produce duplicates (Such as for pindel with default parameters run on the NA12878 Illumina platinum genomic WGS data). Is this intentional, or just an ove…

variantannotation

updated 9.7 years ago • Daniel Cameron

hi, if i have two lists, name A B C and interaction __from   to    InteractionType__ 1        3     0.179539385 2 &nbsp...hi, if i have two lists, name A B C and interaction __from   to    InteractionType__ 1        3   &…

software error R

updated 9.9 years ago • Angel

against DN1620_polar.mzXML ... Found gaps in scan times of the center sample: cut scantime-vector at NA seconds. Found gaps in scan time of file BN_amide_090.mzXML: cut scantime-vector at NA seconds. Error: BiocParallel...arranged in folders by site. # Within each species folder, there should be two folders, one named "Sample" containing all samples for that species # And the …

xcms adjustRtime parameters scantime error biocparallel error

updated 6.3 years ago • abrsoule

div class="preformatted">I am looking for a way to convert geneid to gene name. Specifically, I am calling for variants and then using VariantAnnotation to output using a predictCoding() function...CONSEQUENCE" "REFCODON" "VARCODON" "REFAA" "VARAA". I am interested in gene name moreso than GENEID and so I have been looking at how to do this including using the biomaRt p…

VariantAnnotation convert biomaRt VariantAnnotation VariantAnnotation convert biomaRt

updated 13.0 years ago • Matthew Liebers

plotBCV which has a legend included in the top-right corner of the plot. I would like to change the names in the legend because when I reduce the size of the plot to export it to pdf, the names in the legend goes out of the box. I tried

edger plot Tutorial

updated 7.4 years ago • Juan

files, importer, geneIdCol, abundanceCol, : all(c(geneIdCol, abundanceCol, lengthCol) %in% names(raw)) is not TRUE In addition: Warning message: Unnamed `col\_types` should have the same length as `col\_names`. Using smaller...way? * If using only one file, should I us eit in a diff way? * Maybe the file must be zipped? * Maybe it must have this suffix: "genes.…

tximport RSEM import error

updated 5.4 years ago • harelarik

TSB02184",..: 1 1 1 1 1 1 1 1 1 1 .. (Note: I did import the segments data with FileName as a vector instead of a factor as well. No difference in the error below). I followed the vignette to the letter and, at the end of the...dist(filteredrs) Error in as.vector(data) : no method for coercing this S4 class to a vector > sessionInfo() R version 3.4.0 (2017-04-21) …

software error cntools

updated 7.6 years ago • julianstanleya

lt;- getUniqueCleavageEvents(bamfile, umifile, n.cores.max = 1) Error: subscript is a logical vector with out-of-bounds TRUE values Traceback: 1. getUniqueCleavageEvents(alignment.inputfile = bamfile, umi.inputfile...4. asMethod(object) 5. GAlignmentPairs(ga[first], ga[last], isProperPair = isProperPair, . names = names(ga)[first]) 6. is(first, "GAlignments") 7. ga[first] 8. ga…

GUIDEseq

updated 4.9 years ago • Tiffany

package: limma > maQualityPlots(beta7) Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double' > > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_IN

arrayQuality arrayQuality

updated 12.0 years ago • Saket Choudhary

seqnames strand cigar qwidth <rle> <rle> <character> <integer> [1] hg19_ensGene_ENST00000237247 + 75M 75 [2] hg19_ensGene_ENST00000371036 - 75M 75 [3] hg19_ensGene_ENST00000371037...2580 ... 999 Now, for whatever reason, I would like to …

Coverage genomes Coverage genomes

updated 12.7 years ago • Stefanie

<div class="preformatted">Dear Gordon, I am analysing a simple two-colour microarray experiment camparing strain A vs. strain B with 3 biological and two technical replicates (dye swap). Hence, my experiment is similar to your example in section 11.1 of the limma user's guide. Our array has four within-array replicate spots for each gene. As the "block" argument in the limma function "lmFi…

Microarray limma Microarray limma

updated 20.3 years ago • Pie Muller

1/16, -1/16, -1/16, -1/16)) Error in checkContrast(contrast, resNames) : numeric contrast vector should have one element for every element of 'resultsNames(object)'</pre>   When I remove one \`-1/16\`, it seems to be working...group's information at one point. \`coldata\` contains 17 groups in \`condition\` column. I know I must've committed a mistake somewhere, but I'm n…

deseq2

updated 7.8 years ago • v.t

terms for labels theTerms = as.character(sapply(mget(nodes(testG), GOTERM), Term)) #get the terms names(theTerms) = nodes(testG) #name the terms # 2. set up graph parameters graph.par(list(nodes=list(label=theTerms, shape='rect', fontsize...length(GOlist)) # set a shape for the sigCats sizeList <- rep(42, length(GOlist)) # set a character size for the sigCats names(sigCol) <- name…

GO graph GO graph

updated 13.8 years ago • Iain Gallagher

Hello again, I'm working on the RnaSeqGeneEdgeRQL workflow at the moment, trying to edit it so that it uses my own data rather than importing published RNASeq data from SRA... I was wondering if there is any easier way to do it. The original instructions to create the vector were: (If I got it right, basically, I have to act so that my all.fastq object contains my own data rather than usi…

rnaseqgeneedgerql shortread Rsubread

updated 6.7 years ago • Raito92

Hi,  Basically we have a spreadsheet containing all our microarray data, genes in rows and samples in colums. We have 6 batches in total, each containing 5-8 samples (53 samples in total) that were run on 5 different microarrays. I also created a SIF.csv file containing 3 columns : Array, Sample, Batch (See head and tail below). Array goes from 1 to 6, Batch goes from 1 to 6 and sample …

combat software error

updated 10.6 years ago • kimyoorin1

quehist1[['AH29884']]` line). The error printed was: Error: failed to load resource name: AH29884 title: E003-H3K4me3.narrowPeak.gz reason: 1 resources failed to download 9.stop("failed to load resource", "\n...name: ", names(x), "\n title: ", x$title, "\n reason: ", conditionMessage(err), call. = FALSE) 8.value[[3L]](cond) 7.tryCatchOne(expr, names, parentenv...2.quehist…

AnnotationHub

updated 5.3 years ago • ben.ponv

1. I am trying to add gene names to my result table from DESeq2 using the mapIds functions as outlined in the tutorial for differential analysis of...However I get the message:  " could not find funtion "mapIds""   How do I add gene names to my table?   2. Is there a way to add the gene names to the dds generated using the DESeq2 function:  dds = DESeqDat…

deseq2

updated 10.3 years ago • mtsompana

for every conversion. Is anybody aware of an R-package or script which supports "offline" gene name conversion, i.e. based on previously downloaded gene name database files (disk space is no problem)? Many thanks, Rainer

biomaRt DAVIDQuery biomaRt DAVIDQuery

updated 16.0 years ago • Rainer Tischler

very much for the valuable feedback! Yes, the function expects peak.ranges to be a RangedData with a "names" field as the name of the binding site. I will add your fix to make sure the function works when "names" field is not set. Thanks...space(myPeakList)), > start(myPeakList), end(myPeakList)) > colnames(z1) = c("name", "chr", "peakStart", "peakEnd") > &a…

ChIPSeq chipseq ChIPSeq chipseq

updated 16.0 years ago • Julie Zhu

do: library(Homo.sapiens) txs <- transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene) head(names(txs)) ## [1] "1" "10" "100" "1000" "10000" "100008586" names(txs) <- mget(names(txs), org.Hs.egSYMBOL, ifnotfound=NA) head(names(txs)) ## [1] "A1BG" "NAT2...ranges strand | tx_id tx_name ## <rle> <iranges> <rle> |…

Organism GenomicFeatures Organism GenomicFeatures

updated 12.9 years ago • Tim Triche

of translated transcripts that contain the amino acid patterns I am interested in. Here are their names:> names(cds_seqs[i]) [1] "uc001ack.2" "uc001acv.3" "uc001adm.3" "uc001ado.3" "uc001adp.3" "uc001adq.3" "uc001adr.3" "uc001aee.1...uc009vle.1" "uc001ajj.1" "uc001ajk.1" [19] "uc001ajy.2" The question now is how do I go from these names to conventional protein names and (or) ENTREZ id…

GO GO

updated 13.7 years ago • Zybaylov, Boris L

MC-0-1_GL0117883, LUJU01000040.1.orf00130, 2-1_GL0024467, I need to convert those name, to protein names that I can understand! Is there any package that I could use to convert these names? Please any help will

annotation

updated 5.2 years ago • mercedes.davalos-salas

<div class="preformatted">Hi, I'm using cellHTS2 for a large siRNA screening project and want to rename the channels. The cellHTS instance I created has the default names: > channelNames(x) [1] "Channel 1" "Channel 2" "Channel 3" "Channel 4" "Channel 5" "Channel 6" [7] "Channel 7" "Channel 8" The documentation in version 2.22.0 of Package 'cellHTS2' is: channelNames<-(obje…

cellHTS cellHTS2 cellHTS cellHTS2

updated 12.7 years ago • Mark Dane

Fst(MySample, MAttrib) Error in Fst(MySample, MyAttrib) : STRING_ELT() can only be applied to a 'character vector', not a 'NULL' > sessionInfo() R version 3.0.1 (2013-05-16) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE

genomes genomes

updated 12.3 years ago • Voke AO

ranges(vcfRange), + ref = vcfRange$REF, + alt = vcfRange$ALT) Error in as.vector(x, mode = "character") : no method for coercing this S4 class to a vector ``` This is how I obtained the vcf example: ``` >library(VariantAnnotation

vcf somaticSignatures Vrange

updated 6.7 years ago • maisapinheiro12

Hi, This is a question about R.  I try to assign a vector to a data.frame with name 'in' and got error: Error: unexpected 'in' in "refseq$in" I just want to know why I get this error? Thank

data.frame

updated 10.3 years ago • qiuworld.ou

it works just fine. Also, here's a suggested improvement - at least for 'marrayRaw' objects, sample names don't currently get used. I added the following to the getdata function to so the samples will be labeled: }, marrayRaw = { if...tmp[, (1:nrslides) * 2] = arraydata at maRf - arraydata at maRb tmp.names = vector(mode = "character", length = 2 * nrslides) …

Biobase affy marray convert made4 Biobase affy marray convert made4

updated 20.1 years ago • Jenny Drnevich

processStrand("-", bam) : ERROR: Mate selection for - strand is invalid "WT_bams" is just a character vector with the names of bam files. It's challenging for me to figure out even which read in the bam file is causing

nucleR

updated 5 weeks ago • efoss

MoEx-1_0-st-v1.text.cdf', species='Mus_musculus') Reading CDF file. Error: cannot allocate vector of size 1 Kb Execution halted </div

cdf cdf

updated 16.0 years ago • Peng Yu

the number of samples that are present in each file." Samples are 4 "n.features*n.data must correspond to the total number of lines to be read from each file. " 8*4=32 But I have 96 lines of data? Do I have to make each technical...own feature? How then would I indicate that they are replicates if they each have their own feature name? I can't reuse feature names because I ca…

HTqPCR

updated 2.3 years ago • Ed Siefker

I am trying to know gene names from a heatmap made by heatmap. 2. Since I have many genes, the gene names (row labels) are not readable. I typed following. Please...teach me how to know gene names from heatmap. data <- read.table("sample.txt") data <- as.matrix(data) out\_f <- "cluster2.png" library(gplots) heatmap.2

R

updated 8.6 years ago • nakanomasayuki265

doing it right, according to the documentation:  factor -> contrast = the 3-element vector  numeric -> name = the character name of the numeric  more than 2 levels -> rerun DESeq with "LRT" as test and then

deseq2

updated 9.2 years ago • Federico Marini

with mzID but addIdentificationData() gave an error (Error in split.default(x, g) : first argument must be a vector). So far I have only been able to read mzid files generated by MSGF+ - but MSGF+ is missing some features I need so I...reading Hela\_120min\_500ng\_retry.mzid... DONE! Error in split.default(x, g) : first argument must be a vector

MSnbase

updated 8.2 years ago • lau1

<div class="preformatted">Dear Bioconductors, Now my problem is as follows: First of all, I read the microarray .gpr files to RGlist, then normalized it to MAlist. After that I convert the MAlist to exprSet for further analysis. Now, I want to filter genes in exprSet according to the names or probeID, but I found there is no geneNames Slot for my exprSet. How to find or keep the geneNames …

Microarray convert Microarray convert

updated 19.3 years ago • yanju@liacs.nl

dba(data, bSummarizedExperiment=TRUE) Error in FUN(X\[\[i\]\], ...) :   assay rownames() must be NULL or equal rowData rownames() / rowRanges   names() Any suggestions? &nbsp

DiffBind

updated 9.3 years ago • svohra

div class="preformatted"> Hello, I am trying to convert a file of gene names to corresponding affy probe names. I managed to write a script that puts the genes in an array then I use the feat = getFeature...mart = mart) in biomaRt however I seem to hit a snag when there is more than probe for a gene name. Does anyone know of an existing script that can do this? thanks Ruppert ________________…

probe convert biomaRt probe convert biomaRt

updated 17.6 years ago • Ruppert Valentino

Biostrings") > human_protein <- readAAStringSet("HUMAN.fasta","fasta",use.names=TRUE) > names(human_peotein[[1]]) > > When I use the function 'names' to extract the name of first name, it > returns 'NULL', but it do have a...and [ on a list-like object: x <- list(A=1:3, B=c(x=1, y=2), C=NULL, D=2:-1) 'x' is a named list: > names(x) …

Cancer Biostrings Cancer Biostrings

updated 12.2 years ago • Hervé Pagès

Dear maintainer, I notice a slightly strange behaviour of readVcf when `` ScanVcfParam(info=) ``. It seems that the imported VCF object somehow retains memories of the original VCF header (in the file), while the data was effectively dropped. After import, the `` show `` method seems fine (header and INFO state that only the desired field was imported). However, looking directly at `…

VariantAnnotation

updated 9.4 years ago • kevin.rue

Hello, I am trying to analyze methylationdata from TCGA Illumina 27k methylation arrays. I am using read.metharray from minfi to import the data and it creates a RGChannesSet: > rgSet27 class: RGChannelSet dim: 55300 295 metadata(0): assays(2): Green Red rownames(55300): 10008 10010 ... 7650762 7650767 rowData names(0): colnames(295): 43212070…

microarray methylation illumina27k minfi

updated 6.8 years ago • laurenz.holcik

object with 15693 ranges and 2 metadata columns: seqnames ranges strand | name score <rle> <iranges> <rle> | <character> <numeric> [1] Scaffold307346 1-165 + | Scaffold307346-1 1 [2] Scaffold107276 94-216 + | Scaffold107276...ape_5.6-2 …

Annotation

updated 3.0 years ago • stacy.genovese

fiveUTRs = fiveUTRsByTranscript(txdb, use.names = TRUE) names5UTR = names(fiveUTRs) cds = cdsBy(txdb, "tx", use.names=TRUE) namesCDS = names(cds) names5UTRCDS = intersect(namesCDS,names5UTR) fiveUTRs...for (i in 1:length(names5UTRCDS)){ x = GRangesList(c(unlist(fiveUTRs[i]),unlist(cds[i]))) names(x) = names(fiveUTRs[i]) fiveUTRCDS = c(fiveUTR…

annotation concatenation GRangesList GenomicRanges

updated 6.8 years ago • anmej

<div class="preformatted">Hi everybody. I am currently using rtracklayer a lot, but I am experiencing some problems with the names of the trackas and tables. For example, I wanted to query the NKI Lads track, which is a hg18 liftover available from the UCSC browser. I do the following: > s <- browserSession() > genome(s) <- 'hg19' > tn <- track…

rtracklayer rtracklayer

updated 12.9 years ago • Gustavo Fernández Bayón

flowAI on some flow cytometry data with ~250k events, however I keep getting this error: _Error: vector memory exhausted (limit reached?)_ I've looked it up and it's likely something that has changed since R 3.5 with the introduction...R freezes and needs a restart. <s>My data isn't long enough to cause this error (26Kb), so it must be an issue with the QC report generated</s>. Upd…

flowAI

updated 7.4 years ago • crostomily

and counts) and was wondering if there is a better way to read my individual counts data so the path name does not show as a sample name. It is starting to get annoying and I am afraid it will mess with downstream analysis. Below

edgeR

updated 23 months ago • aa.machado001

hgu95av2probe):199084 and length(pbn): 201800 don't match?!! There are more sequences than probe names?! I am including code snippet. Thanks, Hrishi data(hgu95av2probe) > summary(hgu95av2probe) sequence x y Probe.Set.Name...Min. : 1.0 Length:199084 Class :AsIs 1st Qu.:161.0 1st Qu.:161.0 Class :AsIs Mode :character Median :319.0 Median :…

probe probe

updated 20.8 years ago • hrishikesh deshmukh

as.is=T) colnames(gff)<-c("chrom", "source", "type", "start", "end", "score", "strand", "phase", "name") gff\_gr<-makeGRangesFromDataFrame(gff, keep.extra.columns=T, ignore.strand=F, seqnames.field="chrom", start.field...nbsp; |      source        type        name   &…

riboseqr ribosome profiling

updated 9.8 years ago • alper.celik

Hi, I noticed that the VRanges class doesn’t allow to set the strand to minus in some cases. For example when creating an object or when changing the start/end. (examples below) I saw [this]() from 5 years ago that seems to suggest that a mutation in the negative strand canot be used in VRanges. Is there a reason to restrict variants to only ’\*’? ``` r suppressPackageStartupMessages(l…

VariantAnnotation

updated 6.0 years ago • david.mas

package to plot pathways with moderate success. When I am working with ~100 nodes, the gene names are included on my final plot. However, when I have larger datasets (~300 nodes) the names disappear. I am using the same method...to obtain gene names and the same parameters to add them to the plots. Does anyone know how to solve this? ```r ##Plot parameters nA <- makeNodeAttrs

KEGGgraph

updated 2.6 years ago • hilarius_bookbinder

set operations (union, intersect, setdiff) on DNAStringSets, but doing so strips off the names. How can I do set operations while keeping the names intact

biostrings

updated 9.6 years ago • nicholasbauer

div class="preformatted">An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070803/ 4460b4ba/attachment.pl</div

updated 18.4 years ago • carol white

Hi. I am trying to make sense of a previously written DESeq analysis which uses the “name” parameter to obtain results. A sample code is below, the first two lines are straightforward - making the Input file and...Hi. I am trying to make sense of a previously written DESeq analysis which uses the “name” parameter to obtain results. A sample code is below, the first two lines are straightforward -…

deseq2 rnaseq

updated 8.2 years ago • muratcokol

am attempting to return the ENTREZ id with the following code (where rownames(topGenes$table) is my vector of Ensembl IDs): egIds <- unlist(mget(rownames(topGenes$table), org.Bt.egENSEMBL2EG, ifnotfound=NA)) This returns a named...vector but it contains Ensembl IDs that were not in my query. setdiff(names(egIds), rownames(topGenes$table)) [1] "ENSBTAG000000375581...happening? The IDs …

updated 14.4 years ago • Iain Gallagher

frame dim(df)= 29 20664. It contains mutation and copy number variation data for genes. The column names are actually gene names. The column names currently are gene1, gene2 .... gene20664. __How can I change the column...names from 1 to 19862 as gene1\_mut, gene2\_mut ... gene19862\_mut __ __and from 19863 to 20664 as gene19863\_CNV, gene19864..._CNV..... gene20664\_…

annotation

updated 10.0 years ago • qurrat.ulain

rowData(vcf) loc <- locateVariants(target, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, AllVariants()) names(loc) <- NULL out <- as.data.frame(loc) </pre> Is there anyway to have, for each variant, the sample or samples that have that

annotation variantannotation sample

updated 10.6 years ago • by0

extend = extend, shift = shift, uniq = uniq, window_size = ws) Error in strsplit(file, "/") : non-character argument</pre> --- I uploaded my bam file named "reads1" using readGAlignments in R. Later I come across this error

medips bsgenome medip-seq

updated 7.8 years ago • vjain

a couple of tables from UCSC using rtracklayer and I wanted to know if I need to add 1 to the column named exonStart (after a suitable splitting - it is a comma separated character list). Kasper </div

rtracklayer genomes rtracklayer genomes

updated 16.6 years ago • Kasper Daniel Hansen

about my gene list, but I always get the same error message posted below. The keys "t1" is a character vector with ensembl gene id list. Could someone tell me what is wrong? <code>> geneinfo <- select(org.Rn.eg.db, keys

annotation

updated 9.1 years ago • z.he

contains FPKM and TPM values but I got this error: ``` > tx2gene <- tmp[, c("Gene ID", "Gene Name")] > txi <- tximport(files1, type = "stringtie", tx2gene = tx2gene) reading in files with read_tsv 1 Warning: 59043 parsing failures...scratch/neocircle-samples-20190118/S006493/l.r.m.c.lib.g/k2.a/t/gene.tsv' 1 Coverage no trailing characters .714223 '/scratch/neoc…

tximport

updated 6.9 years ago • HKS

Basically, there's a line in my >>> class >>> definitions to define a class union, namely: >>> setClassUnion('vectorOrNULL', >>> c("vector", "NULL"). Depending on whether that line is included >>> before...gt; Class "vector", directly > Class "vectorORfactor", by class "vector", d…

GO IRanges GO IRanges

updated 12.9 years ago • Stephanie M. Gogarten