Bioconductor Forum

nbsp; I would like to ask if it is possible to change the seqnames of a bam file object, giving a vector of character to the function renameSeqlevels. This is because in order to use the fuction summarizeOverlap or count..._id exon\_number   gene\_name       <integer> <character>  &…

annotation GAlignments bamfileobject renameseqlevels

updated 8.9 years ago • teresati

DataFrame` via `unsplit()`. `unlist()` will coerce back to `DataFrame` but flips the row names, because we're not keeping track of our factor grouping: ```r unlist(split, use.names = FALSE) ``` ``` DataFrame with 4 rows and 2 columns...df[["b"]]) ``` ``` ## Error in unsplit(split, f = df[["b"]]) : ## Length of 'unlist(value)' must equal length of 'f' ``` ```r unsplit(spl…

s4vectors iranges

updated 6.4 years ago • Michael Steinbaugh

div class="preformatted">Hi, I am trying to get the gene symbols and names of genes included in the TopTable. I am using affylmGUI package under R 2.9.1 on windows XP. Even after downloading the

Annotation hgu133plus2 annaffy affylmGUI Annotation hgu133plus2 annaffy affylmGUI

updated 16.4 years ago • Kai Treuner

ENSMUSG00000000001", "ENSMUSG00000000003"), gps=gps) and the error: Error in fix.by(by.y, y) : 'by' must specify valid column(s) In addition: Warning message: In is.na(cols) : is.na() applied to non-(list or vector) of type 'NULL' Stepping

exonmap xmapcore exonmap xmapcore

updated 15.3 years ago • Peter Saffrey

<div class="preformatted">We have been experimenting with a NGS protocol in which we insert sheared genomic fragments into a custom plasmid for sequencing on an Illumina MiSeq instrument. The insertion site of this plasmid is flanked by our own custom barcodes (N7) and ~80 nt Illumina-based adaptor sequence. We then PCR out the insert with barcodes and adaptors for sequencing. Our adaptor s…

Sequencing Cancer Biostrings Sequencing Cancer Biostrings

updated 12.5 years ago • Taylor, Sean D

RNAStringSet(hSeedReg))) > comph = RNA2DNA(comphSeed) > mx = matchSeeds(comph, s3utr) mx is a vector of lists: > is.vector(mx) [1] TRUE > length(mx) [1] 676 I would appreciate some help at understanding the results. For instance...on the same line as the miRNA identifier, following the "$" sign. ($`1588`, $`599`, $`9180`;....) It must be an index into something ... …

miRNA miRNA

updated 16.4 years ago • mauede@alice.it

r > read.FCS("G12.fcs", transformation = F); Error in uint2double(splitted, endian == "big") : vector > sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7

read.FCS flowCore

updated 4.2 years ago • Rainer

Dear, everyone. Currently, I am doing find out DMPs in Champ using Illumina EPIC methylation array. And I am doing case-control studies But I got the error message `Error in champ.DMP() : ChAMP.DMP Have not detected even one significant CpGs. You may try other threshold.` Then I found the reason why I got the error message due to the Benjamini-Hochberg correction, and my lowest adjusted p…

DMP ChAMP

updated 2.8 years ago • Seohyun

0 -1 0 0 1 2. *phenoData* (samples_matrix) is a 72 x 8 character matrix with experimental design variables for each chip and block: > head(samples_matrix) Chip Number File Name...colnames(sponge_data))[1] TRUE 3. *annotation* is (annotation_matrix) is a 15744 x 23 character matrix with microarray annotation info, including RefNumber: > h…

Microarray Annotation GO ExperimentData Biobase Microarray Annotation GO ExperimentData

updated 12.2 years ago • Lisa Cohen

I tried to use *coverageByTranscript* function from GenomicAlignments package to calculate the RNA-seq coverage along transcripts. This function requires the exons be sorted in ascending rank (i.e. the first Exxon in the transcript should be listed in the GRanges object first, and so forth, see reference below https://www.rdocumentation.org/packages/GenomicFeatures/versions/1.24.4/topics/cover…

GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript

updated 6.2 years ago • Jiping Wang

Affymatrix ids, I found out that there are multiple affymetrix IDs corresponding to a single gene name for a sample. My work revolves around gene names only. Please suggest the appropriate step to deal with this situation

biomaRt

updated 21 months ago • Reeya

BioMart database will fix it's current Ensembl 47 release with the following attribute/filter name changes involving gene symbols. * For the hsapiens_gene_ensembl (human) dataset you'll need hgnc_symbol as attribute...and filter name to use/retrieve gene symbols. * For the mmusculus_ensembl_gene (mouse) dataset you'll need the mgi_symbol as attribute...and filter name (this was markersymbol in p…

biomaRt biomaRt

updated 18.2 years ago • Steffen

span style="line-height:1.6">Dear all,</span>   I am trying to load a database, which name is in a variable (I actually ask the user to provide the name of the database he needs). Does any body know if this is even possible

library characters

updated 11.1 years ago • Patrick Schorderet

Now that I made sure there are enough sites to allocate all the samples it tells me that the layout must match exactly with the number of samples to distribute on the plates.. ``` r library("Omixer") data(survey, package = "MASS") survey...Error: Problem with `filter()` input `..1`. #> ℹ Input `..1` is `mask == 0`. #> x Input `..1` must be of size 288 or 1, not size 237. Omixer_ind…

Omixer

updated 4.5 years ago • Lluís Revilla Sancho

samplePattern = "PSC", pData = pheno\_data) :   first column of pData does not match the names of the folders containing the ballgown data. In addition: Warning message: In ballgown(dataDir = ("C:/ballgown"), samplePattern...to look at my loaded \_phenodata.csv in R, I see 1st column is 1-38, my samples. 2nd column is the name of the sample dir from my stringtie -e -B  …

ballgown

updated 7.5 years ago • harris

gene_id symbol type <rle> <iranges> <rle> | <character> <character> <character> <character> <character> [1] chr1 10869-11868 + | promoter:1 ENST00000456328.2 100287102 DDX11L1...tx_id gene_id symbol type <…

Annotation annotatr

updated 4.1 years ago • Ahdee

fit) Error: Assigned data `sig$feature <- chi$feature <- phenopath_fit$feature_names` must be compatible with existing data. x Existing data has 2 rows. x Assigned data has 2000 rows. ℹ Only vectors of size 1 are recycled...interaction_sds` and `significant_interactions`. Running these 3 functions, I was expecting to get vectors as stated in the vignette because I only have one …

phenopath

updated 4.6 years ago • Clara

the file is in my working directory. The columns in the rejectedprobes file correspond to and are named exactly as in the CDF file. However, when I try to use RemoveProbes (listOutProbes="rejectedprobes",listOutProbeSets

cdf cdf

updated 19.2 years ago • Dana Wohlbach

AnnotationData AnnotationData

updated 15.7 years ago • Dario Strbenac

2013-02-24 23:17:38 -0800 (Sun, 24 Feb 2013) | 3 lines Tweak to GRanges() constructor so the names of the supplied metadata cols don't run in conflict with some obscure internal argument names. ---------------------------------------------------------------------- -- Means that we can no longer...mycol <- 1 GRanges("chr1", IRanges(1, 10), "+", mycol) And get a GRanges with a metadata c…

updated 12.8 years ago • Michael Lawrence

bioc-issue-bot: ---- Dear @... You (or someone) has already posted a repository with the same name to our tracker. See https://github.com/Bioconductor/Contributions/issues/ You cannot post the same repository more than...once and packages are not allowed to have the same name. If you would like this repository to be linked to issue number: 2675, Please contact a Bioconductor Cor…

Bioconductor

updated 3.6 years ago • Daan

Z70218" "L17328" "S81916" "U63332" "M77235" and I would like to find ( in a repository for ex.) the names as: [1] "hypothetical protein LOC221823" [2] "meningioma (disrupted in balanced translocation) 1" [3] "fasciculation and elongation...to extract almost everything, from locuslink to PMID to FASTA sequences, but the Descriptions (or names)... I've looked in the web and the vignettes of cours…

annotate annotate

updated 19.8 years ago • Giulio Di Giovanni

HMM routine, I have data showing chromosome number and nucleotide position, but no associated gene name or database identifier. e.g. > logRiList[[1]][1:10,] chromosome position end logR state 1 1 10004 10004 0.7627 3 2 1 46844 46844...3 How can I map this data to RefSeq Accession number or EntrezGene ID etc. so I can get the name of the gene asso…

Cancer Breast Cancer Breast

updated 16.7 years ago • Steven McKinney

Symbol or Entrez ID in R? I am using `AnnotationDbi` and org.Hs.eg.db but it seems to give old gene name. For entrez ID 64755, the new gene name is [RUSF1][1] but it gives C16orf58 ```r library(AnnotationDbi) library(org.Hs.eg.db) AnnotationDbi

AnnotationDbi org.Hs.eg.db

updated 4.8 years ago • sgupt46

summary stats, such as the percent positive events, to be drawn onto the xyplot in place of the gate name. I can get this to work fine with the following code for a single file, but I am having trouble getting the results for the...gt; subset = Filename == 327, scales=list(tick.number=10), outline=TRUE, -> names = format(summary(wf[["anothergate"]])$percent …

updated 16.8 years ago • Aric Gregson

using current directory Note: pkgs parameter missing, downloading all packages in repository character(0) > and nothing happens. Alternatively, is there an easy way to get a vector of package listings and define all packages

Biobase edd AnnBuilder Biostrings Biobase edd AnnBuilder Biostrings

updated 21.5 years ago • Peter Baker CMIS, Indooroopilly

I continue to get this error when trying to use biomaRt: my code: Gene_names <- gsessionInfo()etBM(attributes=c('ensembl_gene_id_version', 'ensembl_gene_id','external_gene_name'), filters = 'ensembl_gene_id_version', values = E_Ids, mart = ensemblmart95) resulting error: Batch submitting query [===&…

software error annotation Biomart

updated 6.7 years ago • ericay.scott

remove unnecessary pathway defintions kegg.sets.hs = kegg.sets.hs[sigmet.idx.hs] #creating vector of FCs with Entrez IDs as the names for the gage() function foldchanges = res$log2FoldChange names(foldchanges) = res$entrez...with a dataframe of the results as an input, it only produces 11 enrichment scores (the datatable named out). None of the enrichment scores found match the over/under-r…

KEGG clusterProfiler Bioconductor

updated 2.8 years ago • m-bihie

0 rows into table bgfeature... Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions 1. Make sure you the probes which are labeled +ACI-experimental+ACI- are not the ones with no sequences...0 rows into table bgfeature... Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions Best, Nitesh +AFsAW…

Annotation probe Annotation probe

updated 12.3 years ago • Nitesh Turaga

Is there a way to map Uniprot names (e.g. RASH\_HUMAN) to other identifiers using Bioconductor? I have tried biomaRt, the AnnotationDbi-based packages

uniprot.ws

updated 4.8 years ago • Diego Diez

gt; >> class(BSgenome) > [1] "BSgenome" > attr(,"package") > [1] "BSgenome" >> names(BSgenome) > [1] "Chr01" "Chr02" "Chr03" "Chr04" "Chr05" "Chr06" "Chr07" "Chr08" > "Chr09" > [10] "Chr10" "Chr11" "Chr12" "Chr13" "Chr14" "Chr15" "Chr16...Phytozome (JGI) > | provider version: 3.0 > | release date: January 2010 &am…

BSgenome BSgenome Rsamtools MEDIPS BSgenome BSgenome Rsamtools MEDIPS

updated 11.8 years ago • Vining, Kelly

BSgenome/inst/doc/BSgenomeForge.pdf The genome is forged from a single fasta file which I named `gl34.fa` for the species name and genome version. The instructions speak of assembling a genome from multiple files...and I believe the issue comes from my single file containing all the data. Instead of having a file name for each chromosome, as follows (from the genome used in package examples) :…

cleanUpdTSeq BSgenome BSgenomeForge

updated 6.8 years ago • danielle.bilodeau

bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https...https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES.gz': …

bioconductor installation proxy BiocManager

updated 5.6 years ago • chen

frozen" (i.e. nothing happens but R session is shown as busy), or it gives "Error: cannot allocate vector of size 473 Kb". My system paging file (`pagefile.sys`) grows to 17 Gb (usual size 8 Gb). Session info below. Would be grateful

TCGAbiolinks TCGA

updated 5.3 years ago • aush

Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges

updated 4.5 years ago • rtrivedi1

uses gtf file "gene_id" by default, in the result count table, I have a very big list of MSTRG------ named genes. I would like to know if using an option in featureCount gives the posibility to change from gene_id to ref_gene_id...Would this change be correct? Or maybe I have realized now that there is another option named −−extraAttributes < string > (GTF.attrType.extra) and I can…

featureCount rna-seq gene_id re_gene_id stringtie

updated 7.0 years ago • IRAIA.MAIALEN

my data which has 17816 rows corresponding to genes, and 286 columns corresponding to samples. The name of this matrix is data.matrix2. Some of the first values of this matrix are: data.matrix2[1:3,1:5] GSM36777 GSM36778 GSM36779...I also have the time in which each patient-sample is examined for relapse. This information is in vector y, which has length 286, and is declared in months. Indi…

Survival Survival

updated 17.7 years ago • Eleni Christodoulou

<div class="preformatted">Dear all, I'm working with Agilent 4X44 K human arrays. I have a vector with Agilent probenames that I would like to annotate with biomaRt. I use the following command: getBM(attributes = c...div class="preformatted">Dear all, I'm working with Agilent 4X44 K human arrays. I have a vector with Agilent probenames that I would like to annotate with biomaRt. I us…

Annotation probe annotate biomaRt Annotation probe annotate biomaRt

updated 15.3 years ago • De Boever Patrick

Once you're working with a matrix like 'ex.data', a not so elegant way is by getting the probeset names with... > dimnames(ex.data)[[1]] Then you can pull out the rows(genes) you want from the expression set using a boolean vector...This should give you the expression measure for each chip at the given gene as a numeric vector. _____________ To find out the type of an object called 'ex.…

updated 20.9 years ago • Rhonda DeCook

to use singleR without a reference dataset but instead given a list where each item in the list is a vector with names of genes that are defining each cell type (without there expression value)? I know that singleR is based on

single cell singelR

updated 5.4 years ago • lirongrossmann

plot however with ``` ggcyto(T_Singlets_MyFlowSet, aes(x="BV421-A")) + geom_density_ridges(aes(y=name)) ``` I get an error: ``` Error in max(data$y) - min(data$y) : non-numeric argument to binary operator ``` Could this error occur because my...name" vector in the phenodata dataframe is off the class " 'AsIs' chr" and not "chr" ?? This is at least the most obvious difference for

FlowCytometry flowCore ggcyto

updated 3.3 years ago • alex.hoefs

an object with the result of DESeq2 differential expression analysis algPvalue <-resTable$padj; names(algPvalue) <- rownames(resTable); algPvalue <- algPvalue[names(algUP)]; #### algUP is a vector that contain 10,000 genes (background

topGO

updated 8.8 years ago • colaneri

package to access data in my projects. One thing I miss often is to convert easily UniProt taxon names to scientific species names, like ECOLX to Escherichia coli, or HUMAN to Homo sapiens. Manual conversion is...taxname2taxid() # ECOLX -> 562 taxname2domain() # ECOLX -> B</pre> These works also in vector context, e.g. <pre> > taxname2spec…

uniprot.ws svn git

updated 9.3 years ago • Csaba Ortutay

<div class="preformatted">Hello, I created a filter function to filter the microarray data set by row variance, but got follow error: > dim(data1) [1] 7129 38 > data1[1,2:4] data[, 4] data[, 6] data[, 8] 1 -139 -76 -135 > myfilter<-function(j){ + function(x){ + rowVars(x)<j +="" }=""> > ff<-filterfun(myfilter(2…

Microarray Microarray

updated 16.8 years ago • wxu@msi.umn.edu

<div class="preformatted">Hi, All - I'm confused by the affinities returned by justPlier (from the plier package). My understanding is that the PLIER algorithm is supposed to produce a single affinity per PM/MM probe pair, across the entire set of arrays analyzed. However, justPlier() returns the values in a matrix of dimensions <# of probe pairs> X <# of chips&g…

rae230a cdf probe reposTools affy plier rae230a cdf probe reposTools affy plier

updated 20.2 years ago • Jeremy Gollub

Failed to collect lazy table. Caused by error in `db_collect()`: ! Arguments in `...` must be used. Problematic argument: ..1 = Inf Did you misspell an argument name? Run `rlang::last_trace()` to see where the error occurred

error lazy R biomaRt table

updated 2.2 years ago • Abhishek

<div class="preformatted">Dear all, I read a data set with the command: > Tol.eSet <- read.exprSet("Tolerante_b.txt") and the result is wonderful! > Tol.eSet Expression Set (exprSet) with 2516 genes 18 samples phenoData object with 1 variables and 18 cases varLabels sample: arbitrary numbering Now, I try to …

updated 20.9 years ago • Marcelo Luiz de Laia

<div class="preformatted">On 30-07-2014 10:13, Alex Gutteridge wrote: > On 29-07-2014 10:00, Alex Gutteridge wrote: >> Hi, >> >> I have a time course RNASeq experiment and I'd like to detect DEU >> between early and late stages. I am trying to use 'Age' as a >> continuous variable in my design, but I'm getting an e…

RNASeq TimeCourse timecourse DEXSeq DESeq2 RNASeq TimeCourse timecourse DEXSeq DESeq2

updated 11.4 years ago • Alex Gutteridge

now I want to visualize the results. I want to graph heatplots and cnetplots but reading the genes names/symbols instead their ENSEMBL ID's. Is this possible? If yes, how

clusterProfiler enrichplot

updated 2.8 years ago • GenoMexa

experiment)</pre> with the error message: Saving 7 x 7 in image Error: Faceting variables must have at least one value The traceback is: 10: stop("Faceting variables must have at least one value", call. = FALSE) 9: layout\_base

ChipQC chipqc

updated 9.3 years ago • thekatybrown

the covariates. Error in contrasts.fit(fit, contrast.matrix) : Number of rows of contrast matrix must match number of coefficients In addition: Warning messages: 1: In rn != cn : longer object length is not a multiple of shorter...object length 2: In contrasts.fit(fit, contrast.matrix) : row names of contrasts don't match col names of coefficients I think I don't really understand how t…

updated 14.4 years ago • Belmont, John W

not running the same code for a month or so, I am getting a new error. I am now getting NAs as probe names for datasets using getGEO(). It seems that datasets obtained with platform GPL4372 are having issues but platform GPL2700...GSEMatrix =TRUE, AnnotGPL=TRUE) if (length(gset) > 1) idx <- grep("GPL4372", attr(gset, "names")) else idx <- 1 gset <- gset[[idx]] fData(gs…

GEOquery

updated 4.0 years ago • John

gr, mcols0$type, mcols0$ID, : some transcripts have no "transcript_id" attribute ==> their name ("tx_name" column in the TxDb object) was set to NA 2: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0...ID, : the transcript names ("tx_name" column in the TxDb object) imported from the "transcript_id" attribute are not unique txdb TxDb object: Db type...with 0 columns …

GenomicFeatures

updated 3.1 years ago • oluwamosope

I am using goseq for GO enrichment analysis of mouse RNA-seq data. I have generated the appropriate named vector to begin the analysis - for example, condition1. All elements in condition1 have either a 1 (DE) or a 0 (non-DE) assigned...to them. However, when this vector is passed to the nullp function to create a data frame containing bias and weighting information a substantial \# of...just som…

goseq pwf

updated 10.3 years ago • mjnolte

Hello, All the codes are running well. I tried to plot the enrichment of the GSEA. But it comes out the error. Thank you in advance for great help! Best, Yue > library(fgsea) > library(tidyverse) > library(data.table) > library(ggplot2) > setwd("/media/hp/04c65089-71ff-4b33-9a30-c21b8c77eda2/li/HASM_SILAC/finally/DEP") > …

fgsea

updated 4.9 years ago • yueli7

however biomart ensembl hgnz\_names only contain 19869 out of my 29581 genes. In my dataset, gene names are HUGO, too. It seems that around 10,000 of my genes are not included in the total of 36,713 genes in biomart ensembl. I checked...to see if there is a potential naming difference, but I couldn't find anything incriminating. Does anyone have an idea why that happens? Thanks

biomart ensemblbiomart

updated 8.3 years ago • spr

package cannot properly handle condition (given by the 'sample\_1' and 'sample\_2' columns) names starting with numerics. Some methods handles it standard R style by adding an 'X' before the condition/sample name. Examples

cummerbund

updated 9.8 years ago • kristoffer.vittingseerup

extendedMapSeqlevels() for using GenomeInfoDb when there is information regarding the species and naming style of interest. Otherwise sequence names are left unchanged." - [Source](https://github.com/lcolladotor/derfinder/commit...9739f1242d74315a2ce5e91acc63a74911964caa).   Reading, "otherwise sequence names are left unchanged", I thought rather than take the time to figure out how to …

derfinder GenomeInfoDb GenomicRanges

updated 8.7 years ago • Wayne

hello all, i am doing a differential gene expression analysis using limma, i have 3 conditions S0,S1, and S3. I am creating the contrasts and doing the fit function but its giving the error ( Number of rows of contrast matrix must match number of coefficients in fit) ``` > contrast.matrix <- makeContrasts( + S1_vs_S0 = S1 - S0, + S3_vs_S0 = S3 - S0, + S1_vs_S3 = S…

limma

updated 20 months ago • zzrammal

transcriptId distanceToTSS ENSEMBL SYMBOL GENENAME <character> <numeric> <character> <character> <character> [1] ENSMUST00000146554.1 11108 ENSMUSG00000084966 2810471M01Rik RIKEN...geneChr geneStart geneEnd geneLength geneStrand geneId <rle> <iranges> <rle> | …

downstream Priority ChIPseeker

updated 4.8 years ago • Xiaojie Cheng