Bioconductor Forum

nbsp; <pre> > mae2 A MultiAssayExperiment object of 5 listed experiments with user-defined names and respective classes. Containing an ExperimentList class object of length 5: [1] BRCA_miRNASeqGene-20160128: SummarizedExperiment

multiassayexperiment

updated 7.3 years ago • mario.zanfardino

I get an error: "Error in contrasts.fit(fit,contrast.matrix): Number of rows of contrast matrix must match number of coefficients In addition: Warning row names don't match col names of coefficients" for the following Timecourse...Stimulated (LPS) versus Unstimulated (CON) cells Affy Gene1.0 chips The targets are ChipNumber Name Filename Time Treatment Biolrep 1 …

TimeCourse timecourse TimeCourse timecourse

updated 16.9 years ago • David Martino

1] "http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ENDOCYTOSIS" # # Slot "source": # character(0) # # Slot "design": # character(0) # # Slot "identifier": # character(0) # # Slot "species": # character(0) # # Slot "data": # character(0) # # Slot "private...character(0) # # Slot "creator": # character(0) # # Slot "ids": # [1] "F2R" "EPN3" "IQSE…

PGSEA smc object

updated 8.0 years ago • da.de

I have a paired-end RNA-seq data in bam. It was read into R using readGAlignmentPairs, named gal2. The compatible reads pairs was parsed using findCompatibleOverlaps function. The following codes only specifically...ranges strand | exon_id exon_name <rle> <iranges> <rle> | <integer> <character> [1] chr1 94458394-94458798 - | 18097 …

GenomicAlignments RNA-seq paired-end read coverage

updated 6.4 years ago • Jiping Wang

I am trying to det telomere length values from processed dna methylation data. I am using the package methylclockdata the code I used is as follows: ```r library(minfi) library(knitr) library(limma) library(minfi) library(IlluminaHumanMethylation450kanno.ilmn12.hg19) library(IlluminaHumanMethylation450kmanifest) library(RColorBrewer) library(Gviz) library(stringr) library(ENmix)…

methylclockData minfi methylclock minfidata

updated 22 months ago • sharangiiv

want. Remember the second parameter in geneAnswersBuilder is annotationLib that requires either the name of given annotation library file or user provided annotation list? So you need to provide an annotation list for GO terms...where the name of each list element is a GO term and each list element contains a vector of TAIR IDs. Instead of using Entrez gene IDs, you...Error in switch(sub("org.\*\…

GeneAnswers annotation Arabidopsis GO

updated 10.6 years ago • lhuang7

5 value columns across 1 space space ranges | stable_id strand phase <character> <iranges> | <character> <integer> <integer> 1 17 [7590695, 7590856] | ENSE00001146308 -1 -1 end_phase <integer> 1 -1 sequence <char…

xmapcore xmapcore

updated 15.4 years ago • Steve Taylor

dir(originDir, full.names = TRUE), pkgdir, > symbolValues, : > > 'symbolValues' must only contain characters. > > Could you please let me know how can fit it? > > Thank you in advance! > > Best regards, &gt

Annotation cdf makecdfenv oligo xps Annotation cdf makecdfenv oligo xps

updated 11.5 years ago • James W. MacDonald

ranges strand | tx_id <rle> <iranges> <rle> | <character> ENSMUST00000029812 3 135584655-135691546 - | ENSMUST00000029812 tx_biotype tx_cds_seq_start tx_cds_seq_end...character> <integer> <integer> ENSMUST00000029812 protein_coding 135585355 135667785 …

ensembldb

updated 4.2 years ago • Michael Love

RNA sequencing (gene's expressions). I am wondering if there is a way to change this package name to be more proper like \`RTCGA.RNAseq\` and if that's possible, how should I do that and to whom should I write

r developers devel

updated 10.1 years ago • MarcinKosiński

<div class="preformatted">Hello, I have assembled transcripts based on unstranded RNA-seq data. It's not the ideal experimental design, of course. Is it not possible to make a TranscriptDb object from this ? makeTranscriptDbFromGFF("transcripts.gtf", format = "gtf", exonRankAttributeName = "exon_number") extracting transcript information Estimating transcript ranges. Extracting gene IDs P…

TranscriptDb TranscriptDb

updated 12.7 years ago • Dario Strbenac

<div class="preformatted">There appear to be different methods available for 'Rle' when loaded via the GenomicRanges package depending on whether a GRanges object has been created. Specifically, prior to a GRanges object being created there are no 'values = character' methods for 'Rle'. This doesn't make sense to me and is causing me problems in code I am developing. The following code hig…

GenomicRanges GenomicRanges

updated 12.9 years ago • Peter Hickey

span style="background-color:yellow">`` Error in i$p.value : $ operator is invalid for atomic vectors ``</span> can't figure out what is possible reason. Can anyone tell me what's going on? How can I fix this bug ? How can I facilitate

r granges dplyr error handling

updated 9.2 years ago • Jurat Shahidin

over 1 hour to BLAST just 10 genes). Currently, the gene identifiers I am using are simply the gene names, but it shouldn't be too difficult to derive a list of corresponding alternative identifiers (assuming they are publicly

Microarray GO Organism PROcess GOstats Microarray GO Organism PROcess GOstats

updated 11.9 years ago • Guest User

feature id exon transcript gene symbol density <rle> <iranges> <rle> | <character> <character> <character> <character> <character> <character> <numeric> [1] chrVIII [212510, 212704] + | CDS unknown YHR052W-A_1...C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton Univ…

Annotation Gviz Annotation Gviz

updated 11.6 years ago • Lance Parsons

For example: "|$COM||$CYT|Partec PAS|" I know, this only works assuming that there are no keyword names that would include the <delimiter_char> as part of the name. I believe that this is a safe assumption after having seen...CYT" (value "Partec PAS"). A strict FCS compatible implementation reads this as a single keyword named "$COM|$CYT" with a value of "Partec PAS". 3) x where x is not a…

Cancer safe flowCore Cancer safe flowCore

updated 13.5 years ago • Josef Spidlen

I can use locateVariants() successfully in Bioconductor 2.10. Due to I can not adjust chr name of txdb to match the chr name of BSgenome, so I can not run predictCoding() in Bioconductor 2.10 for my Arabidopsis TAIR10...same assembly as TAIR9, see Herv?'s reply. library(BSgenome.Athaliana.TAIR.04232008) ## adjust chr name of txdb to match chr name of BSgenome seqlevels(txdb) <- sub("^C",…

Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation

updated 13.2 years ago • sun

div class="preformatted">Dear Anthoula, You are getting an error message from mroast() because the vector of gene weights must be of the same length as the number of the genes in the set, not of length equal to all the genes in your...like explained > in the paper (Wu 2010) generated errors. > > When adding weights as a vector, dimensions did not fit (see below). >…

Cancer limma Cancer limma

updated 14.0 years ago • Gordon Smyth

Sequence unavailable CBL 3;1;2 ENST00000634301 HGNC:1541 ``` So, the column names don't seem to be assigned in the correct order?! Furthermore, there is "Sequence unavailable" and HGNC:1541" instead of cDNA

annotation

updated 5.5 years ago • sarah.sandmann

the 1st column as the common split factor, and then go thru subsetting by the user-supplied 'keys' vector. Here is a simple wrapper to select() that does this but it doesn't know how to handle NAs in the input: selectAsDataFrame...keys0 <- unique(keys) ans0 <- select(x, keys0, columns, keytype) stopifnot(names(ans0)[1L] == keytype) f <- ans0[[1]] if (ncol…

GO Infrastructure Cancer GO Infrastructure Cancer

updated 12.4 years ago • Hervé Pagès

class="preformatted">hi, I would like to easily query the weight (or label) of an edge given its name. e.g. suppose I have a graph 'g' whose nodes are labeled A1, A2, ... I want to do something like: getEdge(g, "A1~A3")$weight Any suggestions

graph graph

updated 15.6 years ago • Gustavo Lacerda

fNames=rep(c("g1","g2","g3","g4","g5"),4) fLoc=sort(rep(c("pos1","pos2"),10)) fData=data.frame(name=fNames, location=fLoc) fDatalbl=data.frame(labelDescription=c("Name of Gene", "Location of Gene"), row.names=colnames(fData...gt; data ExpressionSet (storageMode: lockedEnvironment) assayData: 20 features, 5 samples element names: exprs phenoData rowNames: a, b, ..., e (5 total) varLabels …

ExpressionData ExpressionData

updated 18.5 years ago • Kocherginsky, Masha [BSD] - HSD

csv) in a bioinformatic context. I wonder, if there is a convention on how the "features" are named for DESeq2 csv outputs. In one of my sample datasets for genes for example, genes are named with "geneName.gene". Would an...example for CDS be named "cdsName.cds"? Is the .gene an error and the name column would normally contain only the feature name? Thanks in advance

deseq2 gene format

updated 6.4 years ago • miriam.mueller

I want to change two things in this cnetplot 1. Exclude pathways in the graph 2. Providing gene names instead of the IDs   __1. __Using the example: <pre> require(dplyr) head(kegg@result) %>% select(Description, setSize) Description...__2. __using the example Instead of the ids (such as `` 6891 ``) I want to show the gene names wh…

clusterprofiler pathway analysis pathways

updated 7.6 years ago • Mr.RB

like Error in assay(object, i = exprs\_values) :   'assay(<SingleCellExperiment>, i="character", ...)' invalid subscript 'i' 'i' not in names(assays(<SingleCellExperiment>))   or if I calculate CPM here as  calculateCPM

singlecellexperiment sc3 scater

updated 8.1 years ago • chengyuzou

<div class="preformatted">I have been using RdbiPgSQL successfully for a year or two. I commonly save my queries in text files that I can use either in PostgreSQL's psql (useful for testing and editing) or in R using readLines(). For example (in R): library(RdbiPgSQL) conn <- dbConnect(PgSQL(), host = "localhost", dbname = "agdb") test.sql < readLines("queryfile") test.df &…

RdbiPgSQL RdbiPgSQL

updated 20.3 years ago • William McCoy

parsed.  I believe that this is a bug and the Biostrings should either recognize <cr> characters and parse the file, or trip an error. I can replicate this behavior as follows: 1. save the following fasta using the...pre> readDNAStringSet("~/Desktop/test.fna") A DNAStringSet instance of length 1 width seq …

biostrings software error bug

updated 8.9 years ago • zach.charlop.powers

gnu-library/2.10/Resourcerer/temp /affy_HG-U133_Plus_2' : Aucun fichier ou dossier de ce type* ls() *# character(0)* # Files are created list.files(file.path(.path.package("Resourcerer"), "temp")) *# > [1] "affy_U133Plus2" "file643c9869affy_HG...U133_Plus_2.zip" "README"* * * # You can see the problem is uncorrectly named : temp file was named "affy_U133Plus2" instead …

Annotation Organism Annotation Organism

updated 14.4 years ago • Guillaume Tiberi

Number of significant surrogate variables is: 15 Iteration (out of 5 ): Error in cbind(mod0, uu$vectors[, 1:n.sv]) : number of rows of matrices must match (see arg 2) ---- Is SVA inappropriate for my data because n.sv = 0? And what does it

Microarray sva Microarray sva

updated 12.8 years ago • Shraddha Pai

<div class="preformatted">Hi Steffen et al, Quick question about a search query via biomaRt. Here is the code that I am using: ***** library(biomaRt) ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") filters = listFilters(ensembl) attributes = listAttributes(ensembl) getBM(attributes=c("ensembl_peptide_id", "entrezgene", "ensembl_gene_id", "hgnc_automatic_gene…

GO hgu133plus2 biomaRt GO hgu133plus2 biomaRt

updated 15.9 years ago • Tony Chiang

avgTxLength ... H cooks rownames(11060): FBgn0000003 FBgn0000008 ... FBgn0288846 FBgn0288856 rowData names(66): baseMean baseVar ... deviance maxCooks colnames(198): 1 2 ... 1291 1425 colData names(10): library sample ... condition ``` the 'rownames...an extra column in res_log2FC which consists in a concatenation of the accession number and gene name : genes <- res_log2FC$row gene_name…

DESeq2 ComplexHeatmap

updated 7 months ago • caroline.zanchi

error printed was: ``` downloading 1 resources retrieving 1 resource Error: failed to load resource name: AH32002 title: E001-H3K4me1.fc.signal.bigwig reason: 1 resources failed to download In addition: Warning messages

DFP

updated 4.5 years ago • hxwanghxw

Dear all, I am trying to map gene names to x y coordinates of probes in celfiles. My celfiles belong to gpl1339(S.aureus). I have some gpl1339 annotation files

microarray probe

updated 10.8 years ago • nazaninhoseinkhan

humanKEGG\[1:10\],PR.quantile=0.95) __\[1\] 1 Error in nrow(edges) :   no slot of name "protEdges" for this object of class "Pathway"__ > \#\#For PoTRA.comb: > > results.comb <-PoTRA.comb(mydata=mydata,genelist...humanKEGG\[1:10\],PR.quantile=0.95) __\[1\] 1 Error in nrow(edges) :   no slot of name "protEdges" for this object of…

graphite potra

updated 7.8 years ago • genomic8328

unit(8, "mm")), height = unit(48, "mm") ) print(ha) A HeatmapAnnotation object with 6 annotations name: heatmap_annotation_273 position: column items: 47 width: 1npc height: 31.757299017573mm this object is subsetable...20.0161333333333mm extension on the right name annotation_type color_mapping height Tissue discrete vector user-defined 5mm Diagnosis dis…

ComplexHeatmap Anno Annotation

updated 4.3 years ago • Ashish Jain

with 7 rows and 0 value columns across 7 spaces > space ranges | > <character> <iranges> | > 1 chr10 [1, 10] | > 2 chr18 [1, 10] | > 3 chr2 [1, 10] | > 4 chr21 [1, 10] | > 5 chr3 [1, 10] | > 6 chr5 [1, 10]…

updated 15.9 years ago • Wu, Xiwei

box in the heatmap with ComplexHeatmap ideally I would like to create a block annotation with the name of the sample in it but so far I wasn't able to do it. Also which RGB color is the best to have blue and red and not purple-bluish...simple_anno_size = unit(2, "mm") ) a <- Heatmap(t(mydata), name = "z score", #title of legend …

r rnaseq complexHeatmap annotation

updated 5.6 years ago • camillab.

query': Failed to collect lazy table. Caused by error in >db_collect(): >! Arguments in `...` must be used. >X Problematic argument: \ ..1 = Inf i Did you misspell an argument name

sesameData sesameDataCache sesame ExperimentalHub

updated 2.1 years ago • alos_diallo

data - the result of which is that the data now consists of a single file containing just the probe names and a single value for each adjusted sample. I want to filter out the non-detected miRNA as per the "filterMicroRna" function...file for each adjusted sample and manually adding back in the columns that I lost...I'm sure there must be an easier way. Any input would be greatly appreciated, …

miRNA probe AgiMicroRna miRNA probe AgiMicroRna

updated 15.5 years ago • Segal, Corrinne

<div class="preformatted">Hello list, I am trying to use topGO for GO enrichment analysis. I have data from an array which is still not supported by BioC (maize array). I have a mapping of genes to GO terms named go_list: $TM00000001 [1] "GO:0009058" "GO:0016757" $TM00000002 [1] "GO:0003700" "GO:0007275" "GO:0005634" "GO:0009414" "GO:0016563" [6] "GO:0009737...an array which is still …

Annotation GO topGO Annotation GO topGO

updated 17.3 years ago • Heike Pospisil

not use argument "readable = TRUE" like "enrichGO" function. I have to translate the gene ID to gene name manually. Could you please help me fix this problem? Thank you

annotation

updated 7.0 years ago • huangzhiguang2016

dataframe 10="" 8="" <factor="" and="" columns="" fastq_names="" lane="" line="" line.nested="" names="" rep="" rows="" runscollapsed="" sperm="" with=""> <integer> <factor> <factor> <factor> <factor> <factor> <character> 14120X1_170412_D00294_0311_ACAJ3TANXX_6...after accounting for biological replicates LINE nested within SPERM and REP neste…

deseq2 DESeq nrow == ncol is not TRUE

updated 5.6 years ago • maniermk

DataFrame with 8 rows and 5 columns sample condition patient treatment sizeFactor <character> <factor> <factor> <factor> <numeric> sample1 sample1 WT 1 A 1.047160 sample2 sample2 WT 1 Ct 1.017620 sample3 sample3...treatment_Ct_vs_A" "conditionWT.treatmentCt" If I do: > res &a…

DESeq2 DESeq2

updated 11.6 years ago • samuel collombet

dim: 2000 35289 metadata(0): assays(1): logcounts rownames(2000): INS SST ... DBP MLLT3 rowData names(1): symbol colnames(35289): D101_5_1 D101_7_1 ... TTTGACTGCTAGTG-1_20 TTTGACTGTCACCC-1_20 colData names(6): annotation.l1...logcounts rownames(14046): ATAD3B MTND1P23 ... Human-CD47-cod-opt Cytosine-Deaminase rowData names(0): colnames(8115): AAACCCAAGTCAATCC-1 AAACCCACACCTGTCT-1 ... TT…

R SingleR

updated 2.9 years ago • Shan

3031 chrX [152661471, 152662221] | 3032 chrX [152662571, 152662671] | > names(a) ##n.b. no ranges present for space "chrM" [1] "chr1" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" [10] "chr18" "chr19" "chr2" "chr20...with 6486 rows and 0 value columns across 23 spaces space ranges | <character> <iranges> …

Cancer Cancer

updated 15.1 years ago • Jonathan Cairns

div class="preformatted">Dear Servin, You are mis-interpretting a little what the column names are intended to represent. They are names associated with the arrays, not with files or channels. All the data matrices...R, G, M and A) must share the same set of column names, because all relate to the same set of arrays. When reading ImaGene data there isn't an...obvious choice of array name, so…

updated 19.8 years ago • Gordon Smyth

cds", "cds", "cds", "cds", "cds", "cds", "cds", "cds", "cds", "cds", "cds", "cds", "cds", "utr3")), .Names = "exon.anno") ) , elementType = "integer" , metadata = structure(list(tx.start = 6407435L, tx.end = 6443591L, cds.start = 6407603L...6442793L), .Names = c("tx.start", "tx.end", "cds.start", "cds.end")) ) R> b <- new("IRanges" , start = c(6407548L, 6410954L, 641098…

Cancer IRanges Cancer IRanges

updated 15.5 years ago • Steve Lianoglou

GRanges object with 956 ranges and 4 metadata columns: seqnames ranges strand | name score <rle> <iranges> <rle> | <character> <numeric> [1] X 55737246-55737271 - | ENSRNOG00000029663_1.. 1000.000 [2] 18 31745729-31745750...summarize_annotations( annotated_regio…

GenomicFeatures annotatr genomicFe

updated 4.7 years ago • António Miguel de Jesus Domingues

131L. Error in importCheckExperimentNames(expNames = expNames, dataframes = data) : The names of the data objects in 'data' differ from the names given in the Experiment column of 'configTable'. The format of my configuration...FALSE) View(Vehicle_2) TTR_data <- list(T_1, T_2, Vehicle_1, Vehicle_2) names(TTR_data) <- c("T_1",…

software error TPP

updated 7.0 years ago • kkim369

24 spaces space ranges | gene strand transcript <factor> <iranges> | <character> <character> <character> 1 chr8 [126085394, 126085566] | MYC + MYC_transcript 2 chr8 [126087239, 126087353] | MYC + MYC_transcript...3 chr8 [126088589, 126088742] | MYC + MYC_transcript …

RNASeq Annotation Organism BSgenome BSgenome RNASeq Annotation Organism BSgenome BSgenome

updated 13.1 years ago • Guest User

When I used beadarry and limma packages to perform differential gene expression analysis on the GSE49454 data set, I stuck to this group name and tried a lot of methods. url<-"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49454/matrix/" filenm<-"GSE49454\_series...to perform differential gene expression analysis on the GSE49454 data set, I stuck to this group name and tried a …

limma beadarray illumina

updated 7.6 years ago • 261092095

pm(affybatch) gives a single probe value in each row and adds a numerical suffix to the gene name so that each probe has a unique gene name. Instead, I'd like to extract the pm probes into a matrix that has a single Affy gene...name for a row header and the signal values for all of the pm probes for that gene in the following columns of that row. Some genes...with the ratio of that probe signal…

probe affy probe affy

updated 21.0 years ago • Stuart Brown

across samples. I am running into an error with DESeqDataSetFromMatrix which indicates my variable names and column names are not matching When I investigate this I find that they are matching. Any ideas? > head(sample_info_tab...Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData However when I check that t…

deseq2 normalization

updated 5.7 years ago • ericmalekos

0%Error in quantile.default(M, c(1, 5)/6, names = FALSE) : missing values and NaN's not allowed if 'na.rm' is FALSE</pre> I tried to search where the `` genotype.Illumina `` function

crlmm

updated 8.6 years ago • komal.rathi

matrix of counts. The resulting matrix has 25221 rows and I'm wondering how I can retrieve the gene names for each row.  source("https://bioconductor.org/biocLite.R") biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene") library

rnaseq summarizeoverlaps count matrix

updated 7.9 years ago • johnsonn573

exonHits p "ct_exonHitsm_7841" "ct_exonHitsp_7844" I can use these odd, modified track names, and display the desired: view <- browserView (session, range.to.view, full='exonHits m', dense='ruler', hide=trackNames (session

trigger trigger

updated 15.2 years ago • Paul Shannon

<div class="preformatted"> The gene annotation information is usually a list component called 'genes' within the output object from lmFit, and eBayes. This gets used in the construction of the table of the top-ranked genes using topTable. Have a look at fit2$genes (for your object fit2). Your R expression has just provided a logical vector of corrected p-values for genes <0.05 base…

Annotation limma Annotation limma

updated 20.9 years ago • Marcus Davy

<div class="preformatted">Hello everyone, I am looking for some help in setting up an analysis protocol in R for my microarray dataset. My knowledge of R is still somewhat rudimentary, but, having worked with it for about half a year now I do understand the basics and can get most of the packages that I've needed to work. However, the past week I've been stumped on a certain analysis that …

Microarray cycle Microarray cycle

updated 17.3 years ago • Martin Bonke

organism so I pulled annotation information from NCBI's gtf file, which has the symbols in a column named "gene". This turns out to cause some internal problem in `glimmaMA()` that tries to put the rownames into a column named "gene...efit <- eBayes(vfit) #This works: glimmaMA(efit, dge = dge) #Change SYMBOL column name to "gene" names(dge$genes)[2] <- "gene" names(efit$g…

Glimma

updated 4.6 years ago • Jenny Drnevich

goframeData <- read.table(ANNO_FILE,header=T) universe <- scan(file=UNIVERSE_FILE,what="character") goFrame = GOFrame(goframeData, organism = ORG) goAllFrame = GOAllFrame(goFrame) gsc <- GeneSetCollection(goAllFrame...setType = GOCollection()) genes <- scan(file=GENE_FILE,what="character") NAMESPACE="MF" x = length(NAMESPACE) params <- GSEAGOHyperGParams…

Annotation GO Organism GOstats Annotation GO Organism GOstats

updated 11.8 years ago • Christine Gläßer