Bioconductor Forum

gene symbol. I use ensembl as a database and the human gene set. To find the matching gene names, I use the function getBM and filter it with the probe IDs of my dataset. ensembl <- useMart("ensembl") ensembl <- useDataset...The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. I verify the plateform and its name …

biomaRt

updated 5.8 years ago • ysaboss

in applying these fucntions I have three tabulator delimited text files with my data, labels and names. I have used the read.table function to read the data, and then I have made a list (mylist= list (x=data, y=labels, genenames...names) The summary of this list is something like this: lenght class mode x 25 dataframe list y 25 factor num…

updated 21.6 years ago • Jose Gadea Vacas

gt; uniprotV <- useMart("unimart", dataset="uniprot") > d <- getBM(attributes=c("accession", "name"), mart = uniprotV) Error in getBM(attributes = c("accession", "name"), mart = uniprotV) : Query ERROR: caught BioMart::Exception::Query...200" count = "" softwareVersion = "0.6" requestId= "biomart-client"> <Dataset name = "uniprot" interface = "default…

biomaRt biomaRt

updated 14.2 years ago • kenny daily

the object good. If I use typeof(good), it shows logical. So what I understand is good is a logical vector. But when I type good at the R prompt, it gives me a list of gene name along with TRUE FALSE value. My understanding of logical...vector is that it contains elements which are TRUE or FALSE. So my question is how gene names are accomodated into good. Thanks

updated 22.4 years ago • dibakar ray

code.  Instead of a result, I receive the error message: "$ operator is invalid for atomic vectors." I have modified the code in multiple different ways, but still receive the same error. Any help is greatly appreciated

deseq2

updated 8.2 years ago • jpkarl

in goseq up to date**? I've tried to make my own genome/object for use with goseq. I have a vector of gene names and lengths, but I cannot figure out how to incorporate GO Terms and then make a suitable 'object' that can...1300 fewer genes than my list from sacCer3 (see code). I assume that my provided gene list must have a matching name within `org.Sc.sgd.db` in order for associated GO Terms…

clusterProfiler AnnotationDbi OrgDb goseq

updated 4.9 years ago • vanbelj

idx], + DataFrame(colData(pickrell)[idx,]), ~ 1) Error in names(x) : no slot of name "NAMES" for this object of class "SummarizedExperiment" I am trying to figure out the problem, it seems that...ranges strand | exon_id exon_name <rle> <iranges> <rle> | <integer> <character> [1] X …

deseq2

updated 5.6 years ago • zhangdy1996

minscore = 4){ # fields = c("qname", "rname", "pos", "cigar", "flag"); # # "qname" is read name, "rname" is chromosome # tags = "NM";# character(); # # # Open the BAM file # { # if(nchar(scoretag) == 2){ # scoretag = toupper(scoretag); # tags = c(tags, scoretag...list",length(levels(bb$rname))); # startlistrev = vector("list",length(levels(bb$rname)));…

log timer

updated 2.9 years ago • Anushka

addGeneIDs(tss_annotated_Peaks, "org.Sc.sgd.db", c("symbol", "genename")) Error: Annotation database must be *.eg.db I can't find any hits on google with anyone else trying to do this. Can anybody make any suggestions? I can see that...the source for addGeneIDs does indeed require the name of the database to be *.eg.db. Is org.Sc.sgd.db simply not in a correct format, and therefore deliberately …

Annotation PROcess Annotation PROcess

updated 13.4 years ago • Susan Wilson

AllVariants()) Error in .mk_isActiveSeqReplacementValue(x, value) : the names of the supplied 'isActiveSeq' must match the names of the current 'isActiveSeq' unlist(mget(vars$GENEID, org.Hs.egSYMBOL

SNP annotate SNP annotate

updated 12.7 years ago • Fabrice Tourre

I have a bunch of Reactome ID that I'd like to annotate with Reactome pathway names. Is there a way to do this through `` biomaRt ``? If not, is `` reactome.db `` my best option? I found this in the package manual: _Mappings

biomart reactome reactome.db id

updated 10.1 years ago • enricoferrero

is this plot function: plotMA3by2 It's great. But it doesn't seem to allow me to assign a file name. And it ignores any jpeg or other device calls before it where i could assign a filename. It is writing to the current directory

limma ASSIGN limma ASSIGN

updated 7.0 years ago • Guoneng Zhong

There are non-negligible differences in the number of differentially expressed genes when the linear regression is performed on a design with or without intercept for factors whose regression should not depend on the intercept. Specifically, I have design matrix with 13 cancer types and the presence of mutation A. Each sample must belong to one cancer type, but it may or may not have a mutation …

limma voom linear model

updated 10.9 years ago • Francesco Gatto

span style="background-color:rgb(255, 248, 220)">rownames( counts ) <- raw.data\[ , 1 \] \# gene names </span> <span style="background-color:rgb(255, 248, 220)">colnames( counts ) <- paste(c(rep("C\_R",4),rep("T\_R",3)),c(1:4,1:3),sep="") \# sample names </span...248, 220)">, value = value) : invalid 'row.names' length In addition: Warning message: Setting row …

edger tibble

updated 8.4 years ago • jattnicole29

and to make heatmaps. However, I can't figure out how to label the rows in the heatmap with gene names as opposed to ensembl IDs. I've tried to add gene names/hgnc symbols to the rlog transform values using bioMart, but I was...255)) Is there an easy way to do this. I would greatly appreciate any advice on how to get the gene names onto the heatmaps. Thanks

deseq2 gplot

updated 10.8 years ago • alchemist4au

should be placed in three backticks as shown below library(DOSE) data(geneList) de <- names(geneList)[1:100] x <- enrichDO(de) barplot(x) library(ggplot2) library(forcats) ggplot(result_reactome_121, showCategory...lab(NULL) + ggtitle("Biological Processes") # Error in barplot.default(x) : 'height' must be a vector or a matri…

enrichplot clusterProfiler

updated 2.5 years ago • Manuela

<div class="preformatted">Hi all, I'm still in trouble with reading data from a text file. I worked on CEL files and run the rma function on them. Then it saved the results as a test file. Now, I want to look at the plots (scatter and boxplot), but I don't want to do them one by one. I know that there must be an easy way to get all the plots. Could anyone help me with that. Then, I wanted …

Microarray limma Microarray limma

updated 21.8 years ago • Jamila Ahdidan

gt;colnames(counts)[6:11]=str_split_fixed(colnames(counts)[6:11],"\\.",6)[,5] Error in names(x) <- value : 'names' attribute [11] must be the same length as the vector [7] ``` The code from the above referenced link looks like

DESEq2

updated 5.8 years ago • chunter

__I am using 100 mb transcriptome to simulate 400-800 million reads for a particular fold change eg. 1.2. I require this for 5 replicates. I have the following questions:__ 1. when i run polyester , its just occupying one core/slot for a particular node on my cluster. Therefore its unable to utilise all the available RAM.  Is polyester multi threaded? Can i make it occupy all …

polyester rnaseq

updated 9.6 years ago • aditya892

unplaced contigs and scaffolds. This means that the `` seqnames: `` line in the BSgenome seed file must be very very long (136762 characters), and I seem to be running into some line length limitation in R that causes this line

bsgenome

updated 11.0 years ago • Ryan C. Thompson

nbsp; But if I knew the name of the file R is missing then I could search for it on my hard drive and copy-paste it into the new R directory.  How can...I ask R to give me a list of all the file names that it needs to run?  Is there a function for that?   I have copy-pasted the script in question below:  What is...row.names(eset); Systematic = as.character…

microarray input files saccharomyces cerevisiae bioconductor

updated 11.0 years ago • Thomas.F.Hahn2

called âhexbinâ > show (res) $genotypes A SnpMatrix with 10 rows and 50581 columns Row names: Rodriguez_Lizard_1240_sequence_1_pileup.txt ... Rodriguez_Lizard_623_sequence_1_pileup.txt Col names: RADid_0000001_depth_39...with 505810 rows and 4 columns snp.names allele.1 allele.2 <character> <dnastringset&g…

SNP Sequencing Annotation snpMatrix snpStats SNP Sequencing Annotation snpMatrix snpStats

updated 12.8 years ago • Tereza Jezkova - personal

object with 1081 ranges and 1 metadata column: seqnames ranges strand | name <Rle> <IRanges> <Rle> | <character> [1] chr1 [ 2, 140000] * | CN4 [2] chr1 [140002, 180000] * | CN128 [3] chr1 [340002, 530000] …

granges genomicranges

updated 8.3 years ago • Bogdan

Ringo and Starr vignette. For example, users should use: Sc:Oct_2003;chr1 to name chromosome 1 in their genome annotation file. Maybe the chr1 naming convention is specific to Nimblgen. 2. Creating the...genome Annotation object with BioMart is a good suggestion, but several things must also be matched up to get the genomeAnno object to look like …

Annotation biomaRt Ringo Annotation biomaRt Ringo

updated 16.0 years ago • Noah Dowell

entrezid <Rle> <IRanges> <Rle> | <character> <character> <character> ENSG00000136997 8 [127735434, 127741434] + | ENSG00000136997 MYC 4609 gene_biotype...seq_coord_system symbol <character&a…

TxDB genomicranges genomicfeatures

updated 8.2 years ago • oolongoni

Dear all, I have a problem with the PSICQUIC package while mapping gene name synonyms. Here are the command lines : \# data fetching tbl.big <- PSICQUIC::interactions(psicquic, species="9606",provider...uniprot\_swissprot\_accession  Please use the function 'listAttributes' to get valid attribute names   I cannot figure out what had changed, since this was working w…

psicquic

updated 10.6 years ago • anais.baudot

my gene list but this happened (My gene list consists of only log2 fold change values with gene names associated) ```r BiocManager::install("clusterProfiler") BiocManager::install("pathview") BiocManager::install("enrichplot...MiTabla.xls", header=TRUE) # we want the log2 fold change original_gene_list <- df$logFC # name the vector names(original_gene_list) <- df$Ge…

Bioconductor BIOCOND clusterProfiler

updated 5.0 years ago • María

having problems with the sampleNames for my CEL files. I have already tried to indicate the sample names in ReadAffy function but it does not help: > nm<-c("sampleA","sampleB","sampleC") > data.test<-ReadAffy(widget=TRUE,sampleNames

updated 21.7 years ago • Vitalina Komashko

hichip annotation # Initialize columns for multiple annotations mcols(hichip)$all_genes <- character(length(hichip)) mcols(hichip)$TSS <- character(length(hichip)) mcols(hichip)$promoter <- character(length(hichip)) mcols...hichip)$all_genes_status <- character(length(hichip)) mcols(hichip)$TSS_status <- character(length(hichip)) mcols(hichip)$promoter_s…

ChIPSeqData interact GenomicRanges HiC

updated 16 months ago • user_bioinfo

language-r">Error in assay(object, i = exprs_values) : 'assay(<SingleCellExperiment>, i="character", ...)' invalid subscript 'i' 'i' not in names(assays(<SingleCellExperiment>)) </code></pre> The code that creates the issue is

splatter singlecellexperiment scater

updated 7.7 years ago • luke.zappia

div class="preformatted">Hello, Can anyone tell me how to display heatmap with gene names instead of Affy probes when displaying heatmap from Affy exprsSet. I looked at the heatmap function and exprs class...but I am at a loss as how to change the name on the heatmap to Gene name instead of Affy ID. I managed to get the geneids as follows : geneid <- mget(geneNames(eset), en…

affy affy

updated 18.5 years ago • Ruppert Valentino

<div class="preformatted">Dear all, I am looking for differentially expressed genes using multtest package, MTP procedure. I am computing raw and adjusted t-test P values (group 1 = 7 samples, group 2 = 3 samples) using bootstrap. R is running out of memory ('Error: cannot allocate vector') when the number of genes (5413) combined with the number of bootstrap iterations (B=10000) produce a…

genefilter PROcess genefilter PROcess

updated 17.8 years ago • Timur Shtatland

plyranges

updated 4.1 years ago • Michael Love

datasetconfigversion="0.6" requestid="biomaRt" uniquerows="1" virtualschemaname="default"> <dataset name="hsapiens_gene_ensembl"><attribute name="hgnc_symbol"></attribute><attribute name="chromosome_name"></attribute><attribute...name="start_position"></attribute><attribute name="end_position"></attribute><filter name="chromosome_name" v…

Alignment convert biomaRt Alignment convert biomaRt

updated 16.1 years ago • steffen@stat.Berkeley.EDU

nbsp;element of the list, attrs is used if there are any attributes for this subgraph. This is a named vector where the names are the attributes and the elements are the values for those attributes.") But nothing I put

rgraphviz

updated 9.3 years ago • steve

Compute the score and the best path for a particular position in the score matrix # nucA: (character) nucleotide in sequence A # nucB: (character) nucleotide in sequence B # row: (numeric) row-wise position in the matrix # col...be added, # if the path is up or left, there is a gap in one of the sequences. # nucA: (character) nucleotide in sequence A # nucB: (ch…

SequenceMatching Rstudio sequencing Alignment

updated 3.2 years ago • chenxinyi

Series GSE138260 Agilent-034879 ADchip_1.0 033934 (Probe name version) In the above GEO Series, I have extracted top genes for differential expression analysis. Some of the IDs are...Series GSE138260 Agilent-034879 ADchip_1.0 033934 (Probe name version) In the above GEO Series, I have extracted top genes for differential expression analysis. Some of the IDs are as...ACUST_4167_PI426418842 Is…

AgilentChip

updated 3.8 years ago • Prateek

extensionObject = obji, doComplete = FALSE, : class “chromVARDeviations” cannot extend class “Vector”: slot in class “chromVARDeviations” must extend corresponding slot in class “Vector”: fails for elementMetadata Error...FALSE, : class “VcfFileList” cannot extend class “SimpleList”: slot in class “VcfFileList” must extend corresponding slot in class “SimpleList”: fails for elementMeta…

Install VariantAnnotation Bioconductor chromVAR

updated 4.4 years ago • Hannah

maker-Contig6333 -snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470| 2 maker-Contig6333...snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42...0.75|8|1603| 3 maker-Contig111…

RNASeq maSigPro a4 RNASeq maSigPro a4

updated 10.2 years ago • Guest User

like to generate a  <span style="white-space:pre-wrap">GRangesList of all gene introns with names. I can make the exon list but I do not see a elegant way do get the introns. any suggestion?</span>   <span style="white-space...tx_cds_seq_end <Rle> <IRanges> <Rle> | <character&…

granges ensembldb GenomicFeatures

updated 8.0 years ago • alessandro.pastore

all_colnames, strict.colnames = strict.colnames) : the DFrame objects to combine must have the same column names I understand the problem (the column names are not the same in gbm_exp and lgg_exp) but I can't

TCGAbiolinks

updated 2.2 years ago • nicolas.tajeddine

affymetrix-provided) annotation package. In the top 100 DEG list, there are many gene names in lower-case letters that I am unable to identify. This includes names such as "shasmar", "tusweyb", "flybler.1" and "nugo". Would

microarray pd.clariom.d.human

updated 8.0 years ago • Antonio Ahn

div class="preformatted">Hi, I need some help with the annotation package: To get the gene name for a given probe I perform something like this: > zebrafishGENENAME$"Dr.19073.2.S1_a_at" [1] "annexin A11a" My question...is: How can I do it the other way around, i.e. get all probes with gene names containing "annexin"? Any hint will be highly appreciated. Cheers, Georg </div

Annotation probe Annotation probe

updated 19.5 years ago • Georg Otto

Please help me to use the function named read.agiMicroRna(). Getting the error given below. ``` > library("AgiMicroRna") > dd=AgiMicroRna:::read.agiMicroRna(targets.micro

AgiMicroRna

updated 6.1 years ago • topijush

div class="preformatted">Dear list, can anybody suggest how could I insert gene names in additional to gene symbols on my topTable generated by limma with my differentially expressed genes? cheers, Marcos

limma limma

updated 16.3 years ago • Marcos Pinho

Does anybody knows which is the easiest way and the appropriate package to retrieve some protein names starting from proteins codes? Example: Q7VYR0 -> GTP-binding elongation factor CAA09473 -> P.69A protein (pertactin

updated 15.8 years ago • Giulio Di Giovanni

nbsp; :   sample.name is not a column in rdata. I've tried to check all objects containing name, but probably I've missed something!   any suggestion is appreciated   chiara

exomecopy

updated 7.8 years ago • chiara.rigobello

that seems to suggest that it is possible to assign peaks to regions other than the default ones, namely microRNAs and tRNAs. However, there is no explanation anywhere in this respect, so I was wondering whether it is an actual...remains present in the documentation as part of the information contained in the resulting vector (it should be Intergenic.Region). Best regards, Roger

chippeakanno

updated 7.9 years ago • Roger

dba.count() and having it derive a merged peakset, the $sites element is a list with one logical vector per sample. These vectors are all the same length as the number of peaks in the merged set. The logical values indicate...and is used internally to support the bCalled and bCalledDetail options in dba.report(). Site vectors are also accepted as parameters to dba.plotHeatmap() and dba.plotPCA()…

DiffBind DiffBind

updated 11.6 years ago • Rory Stark

Hello, I wonder if there is a way to use msaPrettyPrint() with sorted alignement by sequence name without rewriting the output fasta file. I know I can read the output fasta file with python, and re-order the sequences...by the sequence name, but I'm pretty sure there is a quickest way to achieve that. I mean i want to see in fasta file and pdf file (output from msaPrettyPrint

msa alignement output sorted

updated 8.9 years ago • Olorin

I have to make the chromosome name to "4" rather "chr4" because my dataTrack 's chromosome names are numbers without "chr". I read the tutorial, and did the following

Gviz

updated 10.4 years ago • tangming2005

I try to upload my unzipped cel files I get an error message: An error has occurred Cannot allocate vector of size 600.0 Mb Error in assign("RawAffyData" , RawAffyData, affylmGUIenvironment) : object 'RawAffyData' not found Error...mtable) ; Unable to find an inherited method for function "indexProbes", for signature "numeric", "character" Error in strwidth(legend, units = "user", cex = cex): P…

Microarray Microarray

updated 16.0 years ago • Christine Tomlins

from / citation of how it was redone? \* I am looking to map the probe IDs to ensembl transcript names, not just the gene names. The package doesn't have this information (only ensembl gene names). Could I obtain this somewhere

microarray annotation illumina human ht-12 v4

updated 10.2 years ago • VSM

gt;> enrichment. >>> >>> >data(pho_sites_count) >>> >genes<-names(rev(sort(pho_sites_count[,1]))[1:300]) >>> > summary(genes) >>> Length Class Mode >>> 300 character character &gt...genes,specis='hsa') >&g…

Organism KEGGprofile

updated 11.3 years ago • zhao shilin

call: value[[3L]](cond) error: failed to load module Ramp from package mzR value of 'SET_ATTRIB' must be a pairlist or NULL, not a 'character' In addition: Warning message: In fun(libname, pkgname) : mzR has been built against a different

mzR Risa mzR Risa

updated 11.9 years ago • gtsiliki@bioacademy.gr

Error in copySubstitute(dir(originDir, full.names = TRUE), pkgdir, symbolValues, : 'symbolValues' must only contain characters. I'm not sure where to go next. I'm not sure how to fix this as this function is called by biobase, which...Error in copySubstitute(dir(originDir, full.names = TRUE), pkgdir, symbolValues, : 'symbolValues' must only contain characters. Thanks, Matthew [[a…

GO cdf Biobase affy GO cdf Biobase affy

updated 11.8 years ago • matthew vitalone

Hi everyone, Just a small question concerning the visualisation of my gating strategy. I would like to add the gatename to the plotted gates and additionally the statistics. I used the following script, but I can only get the gate names (names=T, stats=F) or the stats (names=F, stats=T). #### load flowSet frames_raw <- lapply(files, full.names=TRUE, alter.names=T, read.F…

bioconductor flowcore flowviz flowstats

updated 9.0 years ago • y.klaver

the relevance of Bioconductor and the BioC2006 conference to the applicant's research. Applications must be provided on a single page in PDF or RTF format with indication of name, e-mail address, scholarship track (student-contributor...tracks will be contacted to certify current enrolled status at time of decision. Applications must be e-mailed to biocworkshop at fhcrc.org. Applications must …

updated 19.6 years ago • Vincent J. Carey, Jr.

storageMode: lockedEnvironment) > assayData: 304497 features, 1 samples > element names: exprs > protocolData > sampleNames: 1031.CEL > varLabels and varMetadata description: > ScanDate: NA > phenoData...gt; ?just.rma() > > ff<-just.rma(abatch,cdfname="huex10stv2hsensecdf") > Error: file names must be specified…

cdf affy affyPara cdf affy affyPara

updated 15.2 years ago • Valerie Obenchain

div class="preformatted">Hi, I must admit I'm quite new to both methylation data analysis and R. I am currently analyzing IlluminaHumanMethylation450k...the argument 'object' in selecting a method for function 'annotation': Error: cannot allocate vector of size 8.0 Mb How could I increase the size allocated to a vector? When I submit only 2 samples the initial code works

updated 14.1 years ago • Magdalena Wozniak