Bioconductor Forum

using the makeTranscriptDbFromGFF() command. I can extract all of the transcripts by gene name. I get a GRanges list with each gene and then 2 columns of metadata including the transcripts ID and transcript names associated...lt;Rle> <IRanges> <Rle> | <integer> <character> [1] chrX [77837901, 7785…

genomicfeatures

updated 10.9 years ago • Jake

Checking for blank lines in DESCRIPTION... \* Checking for whitespace in DESCRIPTION field names... \* Checking that Package field matches directory/tarball name... \* Checking for Version field... \* Checking for valid maintainer...and vignette source...     \* NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters long.     Fi…

R

updated 7.7 years ago • topijush

cell lines not responders to the treatment (responders vs not resonders). Here the sampleTable: Name Cell_line condition cell_line1_rep1 Cell_line_1 RESPONDERS cell_line2_rep1 Cell_line_2 NOT_responders cell_line3_rep1...or interaction terms in the design formula are linear combinations of the others and must be removed. Please read the vi…

DESeq2

updated 4.7 years ago • dequattro.concetta

in the bhc package. Anyone know what I'm doing?  In this case, candidates is a list of gene names that I am extracting from a larger frame of all genes.  Plotting the dendrogram works fine.  `` rawCounts = read.table...0, numThreads=10, verbose=TRUE) ``   `` heatmap(hc2) `` Error in heatmap(hc2) : 'x' must be a numeric matrix   Cheers …

bhc

updated 10.7 years ago • b.curran

phenoData = phenoData ) In R 2.9.2 we are getting the following error message: error in sample names<= tmp value = c (sample 1 sample 2 sample 3) value length (8) must equal sample number in assay data (0). I have a question for lumi

lumi lumi

updated 16.3 years ago • Michal Blazejczyk

<div class="preformatted">Yeah, I have the same problem. There are lots of ready-made search solutions out there, and I hope the list admins eventually adopt one of them. In the meantime, I do my searches "off-line". I downloaded all the archives to my computer and then installed WinGrep (http://www.wingrep.com/). As the name suggests, it allows you to use regular expressions. Furthermore, …

updated 21.9 years ago • Alex F. Bokov

<div class="preformatted"> Dear Sue, I think you conveniently forgot to mention the price for the courses. I haven't been able to find any pricing information on your web site either. I must admit that it makes me slightly annoyed that I have to email you to get the price, to me it indicates some degree of shadyness. I suggest you put your prices out in the open so I don't have to put a lo…

updated 18.9 years ago • STKH Steen Krogsgaard

is labeled in that order in d$samples, and in the levels reported in d$samples$group. If I use as names T80 and T60 d$samples will list them in that order but the levels in d$samples$group will sort them and that changed the

edgeR edgeR

updated 13.7 years ago • Spollen, William G.

<div class="preformatted">Hello all, Is there anyway to retrieve the gene symbols, full names (discription), or other gene information, given a list of Entrez Gene IDs (or the LocusLink) in Bioconductor. Obviously, one...div class="preformatted">Hello all, Is there anyway to retrieve the gene symbols, full names (discription), or other gene information, given a list of Entrez Gene IDs (o…

Annotation Annotation

updated 19.5 years ago • Luo Weijun

entrez <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <character> <character> ENSG00000274229 37.124426506691 -24.7224768163257 2.65930667212744 -9.29658736822098 1.45025771568199e...20 2.67558045966171e-16 SOCS7 30837 ensgid <charact…

deseq2 RNAseq

updated 6.7 years ago • Matthias Munz

Reading CDF File Error in read.cdffile.list(filename) : SET_STRING_ELT() can only be applied to a 'character vector', not a 'list' I searched the mailing list and found a similar error: makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap

cdf oligo makePlatformDesign cdf oligo makePlatformDesign

updated 18.3 years ago • Colleen Doherty

div class="preformatted">Hi I am using the getGene function (biomart package) with a vector of ID : ex : getGene(id = refSeqIDs, type = "refseq", mart = martObj) It works with a vector length of 500 but with a length of 5000 it...return NULL. Besides the vector i need to use has a length of 18000. Is there any limit for the length of the vector ? Thanks for your help. TM -- MOUROT Tabar

updated 19.6 years ago • Tabare Mourot

plot the results library(UpSetR) #tidy the datasets genes <- f[[4]] #numeric vector #selected fc names(genes) <- f[[2]] #named vector geneLIST <- sort(genes, decreasing = T) #decreasing order head(geneLIST) de &lt...names(geneLIST)[abs(geneLIST) > 2] x <- enrichPathway(gene=de,pvalueCutoff=0.05, readable=T)…

r rnaseq bulk GO ReactomePA

updated 5.5 years ago • camillab.

results=.IntersectionStrict2(genes,gal2) tx2reads <- setNames(as(t(results), "List"), names(genes)) ## calculate read pair read_counts=data.frame(count=lengths(tx2reads)) rownames(read_counts)=names(tx2reads) #relist...ignore.strand=TRUE) }else{ tx2reads1=IntegerList(vector("list", length(genes))) left_gal=GAlignments() #empty al…

DegNorm GenomicAlignments

updated 3.6 years ago • Jiping Wang

is OK peaks1 = RangedData(IRanges(start = c(1, 100, 200), end = c(2, 101, 201), names = c("Site1", "Site2", "Site3")), space = c("1", "1", "1"), strand=as.integer(1),feature=c("a","b","f")) peaks2 = RangedData(IRanges(start = c(1, 100, 200), end = c(2, 101...201), names = c("Site1", "Site2", "Site3")), space = c("1", "1", "1"),…

GO BSgenome BSgenome ChIPpeakAnno GO BSgenome BSgenome ChIPpeakAnno

updated 12.6 years ago • Vince Schulz

summarizeOverlaps(exons, LungCancerBamFiles()) Yields: Note: method with signature 'GAlignments#Vector' chosen for function 'countOverlaps', target signature 'GAlignments#GRanges'. "Vector#GenomicRanges" would also be valid...Note: method with signature 'GAlignments#Vector' chosen for function 'countOverlaps', target signature 'GAlignments#GRanges'. "Vector#GenomicRanges" would also be vali…

GO GO

updated 12.6 years ago • Michael Lawrence

this command And this is the output: Error in .wrap_in_length_one_list_like_object(value, name, x) : failed to coerce 'list(value)' to a DESeqResults object of length 1 ## What else I've Tried (which still produce the error) Reordering...In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors &am…

deseq2 software error

updated 6.0 years ago • David Eccles (gringer)

gt; > > - Paul > > Error in as.numeric(hgsid) : > cannot coerce type 'externalptr' to vector of type 'double' > > traceback () > 5: browserView(<s4 "ucscsession"="" class="" object="" of="">, <s4 object="" of=""> class "genomeSegment"&gt

hgu133plus2 rtracklayer hgu133plus2 rtracklayer

updated 16.9 years ago • Paul Shannon

file="DNAcutout1.fa", format="fasta") A DNAStringSet instance of length 3615 width seq names [1] 831 TTTCGGCTGTTTAAGAGTCT...CGTCCACTCGTGTGATAGG chr2L:27661:28491 [2] 760 CCGCGCCAAGAACAACCGTT...AGTAATCATTACAAACTTT...DNAcutout1.fa", species=5, model=4) [1] "The input file is not in FASTA format, or contains characters other than A/a, C/c, G/…

BSgenome BSgenome NuPoP BSgenome BSgenome NuPoP

updated 11.4 years ago • Guest User

Hello, Thanks to a file containing a list of rsIDs, I want to retrieve the name of the gene and transcripts corresponding to each rsID. tool : install.packages('BiocManager', repos='http://cran.us.r-project.org...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://suppor…

BioMart getBM webservice

updated 6.6 years ago • amandinelecerfdefer

PATH/Mus_musculus.GRCm38.86.gtf") txdb <- makeTxDbFromGFF(gtffile, format="gtf", circ_seqs=character()) ebg <- exonsBy(txdb, by="gene") se <- summarizeOverlaps(features=ebg, bamfiles, mode="Union", singleEnd=FALSE, ignore.strand...to TRUE  when grouped by "gene"... I tried to group it by tr…

deseq2 rangedsummarizedexperiment grangeslist

updated 8.8 years ago • layal8785

probabilistically across large biomedical datasets. Although traditional linkage variables such as names or zip codes will be available in some datasets, the software must also handle data that contain only genomic sequences...grants). Thus, there will be synergies between the two projects. __Requirements__: Candidates must have a PhD or other advanced degree in computer science, biomedical inf…

Probabilistic Algorithms Big Data Job

updated 10.7 years ago • Doe, Aimee

function</pre> From all the Googling I've done it seems like this is caused by some non-numeric character somewhere throwing a wrench into things, but I can't figure out where the issue is coming from. I understand I need...to generate the dataset - a matrix of integers (cts\_clean; 33602 rows corresponding to gene\_id names and 32 columns corresponding to samples) and a table containing …

deseq2 R error

updated 7.8 years ago • jamesvsheppard

object with 11583 ranges and 4 metadata columns: seqnames ranges strand | name score itemRgb <Rle> <IRanges> <Rle> | <character> <numeric> <character> [1] chr3 [3151401, 3152200] * | 1_TssA...Tcell_effmem_pblood, start =…

gviz chromHMM

updated 8.1 years ago • gammyknee

seqnames ranges strand | score <rle> <iranges> <rle> | <character> rs55998931 chr1 [10492, 10492] * | 0.115787 rs58108140 chr1 [10583, 10583] * | 0.394721 rs75454623 chr1 [14930, 14930] * | 0.48...NA ... NA NA > ranges (gr) IRanges of length 4 start end width …

updated 12.7 years ago • Hermann Norpois

elementMetadata = NULL, metadata = list()), ranges = new("IRanges", start = 1L, width = 200L, NAMES = NULL, elementType = "ANY", elementMetadata = NULL, metadata = list()), strand = new("Rle", values = 3L, lengths = 1L, elementMetadata = NULL...pe = "both", max.frag = 400L, dedup = FALSE, minq = NA_integer_, forward = NA, restrict = character(0), discar…

csaw caught segfault

updated 7.1 years ago • sorjuelal

Hi. I am very new to bioinformatics/programming. Running the code for the first time *ever* using atena package (following their manual). I got the following error. What am I doing wrong? I have attached my full working screen's screen shot for reference. Thanks a lot. Lalani ''''r In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '', probable reas…

RNAseq R Atena

updated 3.2 years ago • lalanis1

api/search/downloads/alternative... formatting gwaswloc instance... NOTE: input data had non-ASCII characters replaced by '*'. Warning message: In gwdf2GRanges(tab, extractDate = as.character(Sys.Date())) : NAs introduced by coercion...ranges strand | DISEASE/TRAIT SNPS P-VALUE <rle> <iranges> <rle> | <character>…

gwascat r

updated 5.0 years ago • anailis

a) Fehler in validObject(.Object) : invalid class "vsnInput" object: 'subsample' must be a numeric vector of length 1 with values between 0 and 2400. > sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32

updated 17.6 years ago • Markus Schmidberger

Thanks for the bug report. This is fixed in IRanges 1.17.11. Note that the data inside the rle must be a factor. Adding levels to an Rle after the fact doesn't create a factor-Rle. x = Rle(c(2,3,1,2,3,2),rep(2,6)) levels(x) = as.character...2 2 2 2 2 2 Values : 2 3 1 2 3 2 > table(x) 1 2 3 2 6 4 The same is true for a numeric vector. table() on a non-factor argument will drop unus…

IRanges IRanges

updated 13.2 years ago • Valerie Obenchain

When I try and create the topGOdata object, I get an error warning about a zero-length vector. I've recently moved to a Mac (see session info). Previously I had no issues using topGO on a linux box, under R-3.6.3 (with...When I try and create the topGOdata object, I get an error warning about a zero-length vector. I've recently moved to a Mac (see session info). Previously I had no issues usi…

topGO

updated 5.7 years ago • abf

row\_index, \] Error in as.integer(index\[\[i\]\]) :   cannot coerce type 'symbol' to vector of type 'integer' Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem,  : &nbsp...Read failed. Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :   'x' must be atomic > > sessio…

rhdf5

updated 8.6 years ago • filipe

in combine_CompressedList_objects(class(x), objects, use.names = FALSE, : the objects to combine must be CompressedList objects (or NULLs)</pre> Any help about how to solve this / what I am doing wrong is much appreciated :) Thanks...txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene ## needs to have 2 meta columns: score, name exo <- exonicParts(txdb, linked.to.single.gene.o…

genomicranges genomicfeatures

updated 8.1 years ago • Fabian Grammes

results table contrasting conditions A and B in the next chunk. We can do this by using either the `name` or the `contrast` argument. Later on we would be interested in the other contrasts with condition C as well, but for purposes...of illustration I leave that out in this example. ``` dds <- DESeq(dds) # call results() w/ name and contrast arguments res.cont <- results(dds,…

deseq2

updated 6.5 years ago • Vincent de Bakker

geneData) data(geneCov) covdesc<- list("Covariate 1", "Covariate 2", "Covariate 3") names(covdesc) <- names(geneCov) pdata <- new("phenoData", pData=geneCov, varLabels=covdesc) so you have to make up the description...of the variables, as a character vector of the right length; Robert > This works fine, except that the varLabels aren'…

Annotation Cancer Annotation Cancer

updated 22.9 years ago • rgentleman

data and I thought it should be possible to hand "geneIds" and universeGeneIds in the form of probe names (here IPI IDs) to the hyperGTest function. If I do so I always get the error: # Error in getUniverseHelper(probes, datPkg, entrezIds

Annotation probe Annotation probe

updated 17.5 years ago • Johannes Graumann

ranges strand | gene_id gene_name gene_biotype <rle> <iranges> <rle> | <character> <character> <character> ENSG00000268640 12 147052-147377 + | ENSG00000268640 AC026369.1 protein_coding ENSG00000120645...CCDC77 protein_coding seq_coord_system symbol entrezid …

CopyNumberVariation CNVRanger GenomicRanges

updated 3.9 years ago • svlachavas

species='Mus_musculus') >>> Reading CDF file. >>> Error: cannot allocate vector of size 1 Kb >>> Execution halted >>> >>> _______________________________________________ >>&gt

Cancer cdf affy makecdfenv Cancer cdf affy makecdfenv

updated 16.0 years ago • James W. MacDonald

by Xiaogang Zhong, Leslie Cope, Elizabeth Garret and Giovanni Parmigiani. The package is named 'MergeMaid', and it should be available to the public tommorow morning (Eastern US time) Package: MergeMaid Version: 2.0...Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix','ex…

Survival Survival

updated 21.6 years ago • Jeff Gentry

to example bamfile bamfile <- RNAseqData.HNRNPC.bam.chr14_BAMFILES[1] # Exmple transcript name transcript <- "uc001yhh.1" # Get exons for transcript allExons <- GenomicFeatures::exons( TxDb.Hsapiens.UCSC.hg19.knownGene...for my transcript cov <- cov[allExons] # Unlist cov <- unlist(cov) # Turn into numeric vector cov <- as.numeric(cov) …

gviz

updated 9.8 years ago • stianlagstad

tsc2 <- 'hsa:7249' tsc1 %in% nodes (g.mTor) # TRUE tsc2 %in% nodes (g.mTor) # TRUE tsc2 %in% names (edges (g.mTor)) # TRUE tsc1 %in% names (edges (g.mTor)) # TRUE edges (g.mTor)[[tsc1]] # character(0) edges (g.mTor)[[tsc2]] # "hsa:6009" Thanks, - Paul

KEGGgraph KEGGgraph

updated 16.7 years ago • Paul Shannon

score <- list(2:4, 6, 7:8) > data DataFrame with 3 rows and 2 columns ID score <character> <list> 1 A 2,3,4 2 B 6 3 C 7,8 ``` </list></character

S4Vectors

updated 2.3 years ago • Dario Strbenac

genes<-data.frame(siggenes.mrna$Gene.Name) > genes$expr<-siggenes.mrna$Score.d. > > names(genes)<-c("genes", "expr") > names(mirnas)<-c("mirna", "expr") > > dim(genes) [1] 87 2 > dim(mirnas) [1] 10 2 > genes[1:5,] genes expr 1 10386996...in RmiR(genes = genes, mirna = mirna, annotation = annota…

miRNA Annotation RmiR miRNA Annotation RmiR

updated 15.0 years ago • Mary Putt

pattern="FJ.wsp",full = TRUE)<br/> ws <- openWorkspace(wsfile)<br/> gs <- parseWorkspace(ws, name=1, isNcdf = TRUE)</code> But I get an error during parseWorkspace: <pre> loading data: E:/17cy1713_TSK_96wellSet/TestFiles/G1.fcs...nbsp; FL03-A not found in flowData!</pre> If I load in one of these files and check parameter names like this below, I…

opencyto flowcore flow cytometry

updated 7.3 years ago • Andrew Box

<div class="preformatted">I am trying to process the raw data downloaded from: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-380 At the moment of using the function neqc I get the following error: Error in if (sigma <= 0) stop("sigma must be positive") : missing value where TRUE/FALSE needed The problem seems to be in this line: In sqrt(weighted.mean(v, freq) * n/(n...of…

PROcess PROcess

updated 13.0 years ago • Michele

<div class="preformatted">I am trying to process the raw data downloaded from: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-380 At the moment of using the function neqc I get the following error: Error in if (sigma <= 0) stop("sigma must be positive") : missing value where TRUE/FALSE needed The problem seems to be in this line: In sqrt(weighted.mean(v, freq) * n/(n...of …

PROcess PROcess

updated 13.0 years ago • Michele

compress=FALSE)</pre> The problem is that I have many other organisms for which I must do the same. __OBJECTIVE__ How can I automate the export process in a way that the filename of the output matches the object...Scerevisiae$chrVII `` is exported, I want to see __Scerevisiae\_chrVII.fasta__ for the name of the FASTA file. __WHAT I HAVE TRIED AND HAS NOT WORKED__ <…

bsgenome biocgenerics bsapply export

updated 7.8 years ago • ረ

coarse") print(dd) Warning messages: 1: Setting row names on a tibble is deprecated. 2: Setting row names on a tibble is deprecated. 3: Setting row names on a tibble is deprecated. 4...Setting row names on a tibble is deprecated. 5: Setting row names on a tibble is deprecated. 6: Setting row names on a tibble is deprecated. 7...Setting row names on a tibble is deprecated. 8: Setting row names on…

GenomicRanges tidySummarizedExperiment tidyomics GenomeInfoDb

updated 10 months ago • Kateřina

Checking for blank lines in DESCRIPTION... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version field... * Checking for valid maintainer...and vignette source... * NOTE: Consider shorter lines; 188 lines (2%) are > 80 characters long. First 6 lines: …

package development

updated 7.3 years ago • ntueeb05howard

<div class="preformatted">Tophat2 cmd: tophat2 -o path/to --transcriptome-index=/Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensem bl/NCBIM37/Annotation/Genes/genes /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/Bo wtie2Index/genome 001.fastq.gz Cufflinks cmd: cufflinks --output-dir path/to --GTF-guide /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotati…

updated 11.8 years ago • Sindre

Hello everybody, I was wondering, if it is possible/advised to use the fRMA algorithm to also analyse HT\_MG-430\_PM arrays. The Affymetrix website states that: "_The GeneChip HT MG-430 PM Array Plate enables high-throughput expression profiling of 16, 24, or 96 samples at a time using the same industry-standard content as the GeneChip Mouse Genome 430 2.0 Array_". Hence I hope, that I can sti…

frma microarray affiymetrix

updated 9.9 years ago • Matthias Z.

boxplots") Error in as.vector(x, mode = "numeric") : no method for coercing this S4 class to a vector ``` ```r > sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS Matrix

coseq

updated 3.9 years ago • ajwijeratne1

a graph of the pathway g <- pathway(pathway_id) |> mutate(ec = rntoec[reaction]) # Define a vector of node names to highlight nodes_to_highlight <- reaction # Add log fold changes (LFCs) to the graph LFC_vector <- LFCs...Make sure LFCs is a vector with values for each corresponding reaction number g <- g %>% mutate( LFC = ifelse(reaction %in% n…

RStudio ggkegg

updated 2.0 years ago • Ramirj49

experiement. I have a treatment condition which involves a mutant protein (supplied by a plasmid vector), so I essentially have four conditions: 1. Control - No vector, target protein not present in cells (they are knock outs for...the protein) 2. Wild Type - The protein is given via a vector in it's wild type state 3. Binding mutant one - The protein is given via a vector, however it has …

deseq2 DE rnaseq sva combat

updated 9.9 years ago • mbio.kyle

or set `show_col_types = FALSE` to quiet this message. > coldata <- data.frame(files = files, names = subfolder_names, condition = c("A", "A", "A", "B", "B", "B"), stringsAsFactors = FALSE) > coldata …

tximeta

updated 2.2 years ago • kyliecode

and set 2 had 11 samples. Additionally, the first sample did not have an "X" at the begining of its name (the rest of the name is correct). Below is the code that I used to generate this data. Note that I am calling this script via...uniq=TRUE extend=300 shift=0 ws=100 chr.select <- chrm #Get vectors with lists of files and file names files1=list.files(path = filepath1, pattern = "…

medips

updated 10.8 years ago • tptacek3050

updated 14.1 years ago • Fahim Md

plotting an alignment track from sequence data that was aligned to hg19 with non-UCSC chromosome names (i.e. "1", not "chr1"). I _suspect_ the problem is to do with the chromosome names, but I am not sure. My code is as follows...chr1</span>")</code>, the error vanishes and it outputs a plot that is blank except for the plot name on the Y-axis, obviously because my b…

gviz software error

updated 7.3 years ago • laura.k.hilton

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 ``` It there any other...to solve this? I need all my ```~20000``` in ``` values=bg_genes``` ``` class(bg_genes) ----> character table(sapply(bg_genes, class)) ----> character 22287

go r software error R biomaRt

updated 5.6 years ago • morteza.aslanzadeh

file.path(dir, "samples_aga.csv")) sample_metadata_aga # paste0 appends (i.e. adds together) character objects files <- paste0(file.path(dir, sample_metadata_aga$sample), ".this.htseq.out") files file.exists(files...ddsHTSeq_aga) # Filtering and data export resultsNames(dds_aga) res_aga <- results(dds_aga, name = "condition_infected_vs_control") head(res_aga) # Subs…

DESeq2

updated 3.5 years ago • Lucía