Bioconductor Forum

<div class="preformatted">Hi list, I am trying to create a TranscriptDb using GenomicFeatures, but I get an error message. I think there might be something wrong with my gff- file, but I am not sure. I also tried converting the gff-file to gtf, but also get an error. My goal with this is to plot the number of exons per gene. Code: #GFF-file > txdb = makeTranscriptDbFromGFF(file =…

Genetics TranscriptDb GenomicFeatures

updated 11.3 years ago • Jon Bråte

<div class="preformatted">Hi all, I have a table (t) of the following format (first row is the header): A x1 x2 c 1 NA c 2 1002 c 3 NA a 4 1004 b 5 NA c 6 1006 c 7 1007 c 8 1008 b 9 1009 a 10 1010 a 11 1011 c …

updated 16.2 years ago • Hari Easwaran

as well as the wider development and extension of the analytical side of this platform. Applicants must have a PhD degree in Bioinformatics, a solid understanding and at least two years experience in the analysis and management...of high throughput data. A high level of expertise in the use of relational databases, in particular MySQL, is essential, as is experience in molecular biology...or canc…

Cancer biomaRt Cancer biomaRt

updated 15.0 years ago • Claude Chelala

command on Rsubread and have the raw counts matrix for all 24 samples at the meta-feature(gene) level. I was wondering if I should combine my biological replicates before further analysis, namely differential gene expression

differential gene expression biologicalreplicates raw_counts

updated 7.2 years ago • tasnif.rahman

is applied pairwise. Whilst this provides a guideline for which samples differ, it isn't strictly valid according to these forum discussions: [Are pairwise Wilcoxon tests a valid non-parametric alternative to Tukey...s HSD test?](https://stats.stackexchange.com/questions/91663/are-pairwise-wilcoxon-tests-a-valid-non-parametric-alternative-to-tukeys-hsd-te), [Kruskal-Wallis Test …

DMRforPairs

updated 8.6 years ago • gabriel.rosser

read10xCounts(h5file). When I look at the rownames of the sce object (see below), the last 12 gene names are CMO301, CMO302 up to CMO312. These are the 10X genomics CMO tags that are used for tagging cells for cell multiplexing...The CMOs should not be added to the sce object as gene names. I could not find an option in read10xCounts to eliminate these rows (nor were google searches productive). …

DropletUtils droplet

updated 2.0 years ago • pcantalupo

<div class="preformatted">Dear all, I have used edgeR for analyzing differential expression. I also created a smear plot visualizing DGE results (code see below). I'd now like to highlight some genes of interest (they are significantly diff. expressed) in this plot by labeling them; do you know if there's a way to do so? Kind regards, and many thanks in advance, Christine Gl??er ###### …

edgeR edgeR

updated 12.0 years ago • Christine Gläßer

Hello, I have a problem because I have little experience with the tbl_graph format and how to use it well with ggtree (or other script to draw a tree). I have created a tbl_graph (from clustree) of this type (object named trees) ``` # A tbl_graph: 386 nodes and 385 edges # # A rooted tree # # A tibble: 385 × 10 from to from_clust to_clust from_TVD to_TVD count...or other script to draw a tree).…

dendogram ggtreeExtra ggtree annotation Annotation

updated 2.7 years ago • christian.dina

<div class="preformatted">Hello everybody, I am using the hclust() function in R. I have a 2000*12 matrix of expression data. I have created a distance matrix with dist() using Euclidean method. Then in hclust I have used complete linkage method. Now when I am trying to plot the dendogram with pclust method I cannot see the details of the tree. The gene names and the lower parts of the de…

updated 20.1 years ago • madhurima bhattacharjee

ever used biomart to get the ENSEMBL ids for the Affymetrix rat exon array at the transcript cluster level: i.e. library(oligo) exonCELs <- list.celfiles("where the rat CEL files are", full.names=TRUE) affyExonFS <- read.celfiles...ensembl id. I wondered if it might be that affy_raex_1_0_st_v1 summarises at the probeset or exon level, but in that case surely nothing would be retu…

biomaRt oligo biomaRt oligo

updated 13.7 years ago • James Perkins

I have the below code. Which executes twice a `` plot_denisities `` function. Unfortunately, when I execute this function again it plots a completely new picture rather overlap the two plots into one plot. #install if necessary source("http://bioconductor.org/biocLite.R") biocLite("Rsamtools") #load library library(Rsamtools) extr…

rsamtools ggplot2 plot

updated 7.0 years ago • mictadlo

_", replicate), cells, treat, replicate, group) colData$cells <- factor(colData$cells, levels = c("A", "B")) colData$treat <- factor(colData$treat, levels = c("C", "T")) colData$group <- factor(colData$group, levels = c("W", "X", "Y", "Z")) design1 &lt...This seems easy with `design2`, by specifying `coef = 2` (i.e. groupX). In that case, t…

deseq2 model.matrix

updated 6.7 years ago • toddknutson

I can do that in 2 ways: Option 1: desMat <- model.matrix(~0+ DiseaseState) colnames(desMat) <- levels(DiseaseState) contMat <- makeContrasts(D-N, levels= colnames(desMat)) # I'm assuming this groups all disease states in one...now my states are D.T1, D.T2, N.T1, N.T2 desMat <- model.matrix(~0+ Combine) colnames(desMat) <- levels(Combine) contMat <- make…

Clustering Clustering

updated 14.8 years ago • Supriya Munshaw

Cuffdiff fork cuff.res=read.delim(file="/home/user/gene_exp.diff", sep="\t") #notice the column name special character changes. The column used to be #cuff.res$log2.fold_change. for older versions of Cufflinks. cuff.fc...gnames=cuff.res$gene sel=gnames!="-" gnames=as.character(gnames[sel]) cuff.fc=cuff.fc[sel] names(cuff.fc)=gnames <strong>Error in names(cuff.fc) = gnames : attem…

GAGE Cuffdiff gene names

updated 10.0 years ago • user31888

biological pathways between two classes of phenotypes. __I need help with printing out the pathway names for the resulting p-values that are found by miR2Pathway. But after looking at the igraph documentation I still cannot...do it. My code is error free, just hoping for some helpful suggestions.__ Additionally, the pathway names should join the miR2Pathway output, if run with the example datas…

igraph miR2Pathway Pathway page_rank

updated 7.7 years ago • genomic8328

Retrive significant gene IDs (XLOC) with a pre-specified alpha diffGeneIDs <- getSig(cuff,level="genes",alpha=0.05) #Use returned identifiers to create a CuffGeneSet object with all relevant info for given genes diffGenes...values (and corresponding XLOC_* values) can be retrieved from the CuffGeneSet by using: names<-featureNames(diffGenes) row.names(…

RNA-seq / XLOC cuffdiff

updated 5.6 years ago • mg.mahabad1365

the function ReadAffy. The error is reproduced here: Error in validityMethod(object): No slot of name "phenoLabels" for this object of class "phenoData" I don't know what's wrong. Any help appreciated. thanks, suresh _________________________________________________________________

affy affy

updated 22.1 years ago • Suresh Kumar Karanam

Objective how to assign a col-name to an empty header inside a list My data structure Code should be placed in three backticks as shown below ```r results1...Objective how to assign a col-name to an empty header inside a list My data structure Code should be placed in three backticks as shown below ```r results1 &lt...lfcSE stat pvalue padj ``` M…

DESeq2

updated 3.7 years ago • kcm

Hi, I'm getting an error with some topGO code which used to work. The below code is an example, so you should be able to just paste it in: library("org.Hs.eg.db") library("topGO") all_genes <- rep(c(0,1,1), each=10) names(all_genes) <- c("LEF1","FOXJ2","ZNF654","TAL1","ZMYM2","DCAF6","PDP1","ZNF302","TMED4","SLC5A6","PLSCR1","RPL41","MARK1","TMSB10","HES6",…

software error topGO org.hs.eg.db

updated 7.0 years ago • natske

<div class="preformatted">Dear BioC, I tested the combineAffyBatch function in the matchprobes library to merge data from HG-U133A and HG-U133Av2 GeneChips, which seemed to work well for small number of arrays. > f1 <- list.files(path=dir1,".CEL",ignore.case=T,full.name=T)[1] > f1file <- list.files(path=dir1,".CEL",ignore.case=T,full.name=T) > pd1 &am…

cdf matchprobes cdf matchprobes

updated 16.9 years ago • Oura Tomonori

I find that unlisting the GenomicRanges returned from a call to `transcriptsBy` returns a list with names that are gene names... only they are incorrect! Look: > txdb<-makeTranscriptDbFromBiomart(biomart="ensembl", dataset...FBgn00000082 2R [18024938, 18060346] + | 8617 FBtr0071764 ... Arguably, those names on the the GRanges should either all be the same, namely …

GenomicRanges GenomicRanges

updated 13.3 years ago • Malcolm Cook

R/library/liblisting.Rda. > > For example: > > > .libPaths() > [1] "/home/cbrg/validate/myRlibs" "/package/R/2.0.1/lib/R/library" > > library(affy) > Loading required package: Biobase > Loading required...setting it) and the search path for packages. Since all the relevant packages are in the system-level package lib, settin…

affy affy

updated 20.7 years ago • Seth Falcon

<div class="preformatted">Dear All, I have analyzed a dataset for differential gene expression using LIMMA. The requirement was to select probesets with highest value of expression. I notice that there is a change in results for when i filter for probesets before and after performing LIMMA. The logFC and gene list remains the same, only change is in the p-value and B Value, again this is p…

limma limma

updated 13.8 years ago • Ekta Jain

If I use the same format with multiple IDs, it returns an error: ```r Error in vapply(names(filterChunk), FUN = function(filter, values, mart) { : values must be length 1, but FUN(X[[2]]) result is length 2 ``` But if I only gives a

Annotation biomaRt

updated 2.5 years ago • RuBBiT0

<div class="preformatted">Dear list, I'm using ALLMLL data set (from ALLMLL Bioconductor package). This package provides probe-level data for 20 HGU133A (MLL.A) and 20 HGU133B (MLL.B) arrays which are a subset of arrays from a large ALL study. I would like to...Dear list, I'm using ALLMLL data set (from ALLMLL Bioconductor package). This package provides probe-level data for 20 HGU133A (ML…

hgu133a hgu133a

updated 15.5 years ago • Javier Pérez Florido

data("dietswap") a <- rowMeans(abundances(dietswap)) dfs <- data.frame(taxa = names(a), mean_abundance = a) %>% arrange(mean_abundance) %>% mutate(taxa = factor(taxa, levels = rev(unique(taxa)))) p <- ggplot(dfs, aes(x

deseq2

updated 5.7 years ago • wisam.tariqsaleem

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 12.1 years ago • Hervé Pagès

call: .make_BSgenome_seqinfo(single_sequences, circ_seqs, genome, seqnames) error: sequence names found in file '/Users/Geo/BSgenome.Dmelanogaster.6.32.Rcheck/00LOCK-BSgenome.Dmelanogaster.6.32/00new/BSgenome.Dmelanogaster.6.32...Check seqnames. current_SequenceName <- unlist(heads(strsplit(names(dna), " ", fixed=TRUE), n=1L)) names(dna) <- current_SequenceName ### Export …

BSGenome Forge

updated 4.1 years ago • geo.vogler

analysis to identify potential biomarkers. Here is a section of my datasheet: ``` CodeClass Name Accession Epi_FAM1.1 Epi_FAM1.2 Epi_FAM2 Epi_FAM3 Positive POS_A(128) ERCC_00117.1 77244 77495 66892 68724 Positive...1230 ``` When I try to creat the set I get the error Error in rowSums(counts) : 'x' must be numeric, so I cannot proceed…

NanoStringDiff

updated 6.6 years ago • noelleenright

values: phenoData(normData) <- pheno The rownames of phenodata has the samples names: rownames(phenoData(normData)) [1] "GSM437316" "GSM437286" "GSM437305" "GSM437297" "GSM437277" "GSM437282" "GSM437269" "GSM437302...GSM437311" [12] "GSM437218" "GSM437114" "GSM437234" "GSM437165" "GSM437299" But column names of assaydata are file names: colnames(exprs(no…

oligo GEOquery ExpressionSet

updated 6.1 years ago • salamandra

test. For this I need to create a 'GOHyperGParams' object, which has as the argument the name of the annotation package, from which it takes the data regarding Entrez.Gene.Ids and correspondent GO annotation...error ïÛÉÂËÁ × getUniverseHelper(probes, datPkg, entrezIds) : After filtering, there are no valid IDs that can be used as the Gene universe. Check input values to confirm they are the same…

Microarray Annotation GO probe GOstats Microarray Annotation GO probe GOstats

updated 14.7 years ago • UnASM Lab_bi

Done! > </pre> Naturally I've checked that the file in question (C1.sam) exists and is a valid sam file. The program creates a file with a garbage name (eg, '%E7%D4I???') containing just a header line: <pre> chrom win.start reads.gc

seqCNA

updated 9.8 years ago • gnatgoodman

The Genomics and Bioinformatics Group in Research Computing at Boston Children’s Hospital (BCH) seeks to hire a Variant Curator / Bioinformatics Scientist. We are seeking creative people with solid analytical capabilities and programming experience. The group is supporting a strategic initiative at BCH to develop streamlined mechanisms to sequence and identify causal genes in patients participati…

genomics Job

updated 6.8 years ago • shira.rockowitz

<div class="preformatted">Dear Venu, limma requires replicates. Pretty much any statistical testing method requires replicates. You can run lmFit() without replicates, which gives you fold changes, but you cannot go on to compute eBayes statistics or to use topTable(). The same answer has been given to many posts asking this question over the years. I am a bit puzzled what you expect l…

GO limma GO limma

updated 13.1 years ago • Gordon Smyth

R * inst ** byte-compile and prepare package for lazy loading Error in RccViolationException("Class names must begin with a letter: ", : > "RccViolationException" function can not be found Error: unable to > load R code in package...gt; byte-compile and prepare package for lazy loading Error in > RccViolationException("Class names must begin with a letter: ", : >…

TCGAbiolinks R.oo

updated 5.4 years ago • Talip Zengin

in validObject(.Object) : invalid class “SummarizedExperiment” object: 1: invalid object for slot "NAMES" in class "SummarizedExperiment": got class "array", should be or extend class "character_OR_NULL" invalid class “SummarizedExperiment...object: 2: 'names(x)' must be NULL or a character vector with no attributes</pre> The same error occurs if you just take counts: <pre> c…

deseq2 tximport

updated 8.2 years ago • ben

fine for me. However, when I use it now, I get the error, "invalid class “DESeqDataSet” object: 'NAMES' slot must be set to NULL at all time". This can reproduced using the example dataset given on pages 5-6 of the "Analyzing RNA...design = ~ condition) Error in validObject(.Object) : invalid class “DESeqDataSet” object: 'NAMES' slot must be set to NULL at all time</pre>   I …

deseq2 error

updated 10.4 years ago • alextuck

Has anyone tried loading an mzid file generated by Comet/PWIZ into MSnbase MSn Experiment data? I was able to read the mzid file 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...with mzID but addIdentificationDa…

MSnbase

updated 8.2 years ago • lau1

TRUE) In fact, after this step I have noticed that ProbeNames are not matching the right miR names. This happens starting from both the dataset supplied as an example and my own miRNA microarray data. The match is correct

miRNA Microarray Normalization AgiMicroRna miRNA Microarray Normalization AgiMicroRna

updated 14.8 years ago • Paola Ostano

div class="preformatted">Hi All, How can I create a variable with a name identical to the character value of an argument that I passed to the function ? The following lines doesn?t work. Do I have

updated 11.3 years ago • my1stbox

age" "conditiondisease.age" I suppose that `"conditiondisease.age"` is the name I am interested for the disease group. But is `"age"` the one for the control? (since it is the reference level) Or is it age regardless

deseq2 R rna-seq design

updated 4.9 years ago • raquelgarza95

<div class="preformatted">Dear All, I am using the LIMMA package to create 2 contrasts for my data and then calculating the vennCounts of the decideTests from the contrast.fit to be able to create venn Diagrams. The code works fine but the summary(results) shows zeros for all i.e. no gene were up regulated or downregulated. This is not true for my data since toptable output shows Log fold …

limma limma

updated 13.6 years ago • Ekta Jain

2. Constructed comparison matrix > contrast.matrix <- makeContrasts(LineA-LineD, LineB-LineC, levels=design) > contrast.matrix Contrasts Levels LineA - LineD LineB - LineC LineA 1 0 LineB 0 1 LineC 0 -1 LineD -1 0 3. Perform fitting...package and perform comparison I…

Sequencing SmallRNA Microarray limma Sequencing SmallRNA Microarray limma

updated 11.3 years ago • Jakub Stanislaw Nowak

found the setWeights function in beadarray that can save the weights found by BASH to the bead-level object? These weights are multiplied by bead intensities when the bead summary data are created. Currently we tend...of the new version of beadarray (version 2.0 and newer) is that you can save weights under different names in the bead-level object. It should be possible to do a series of tests fo…

Cancer beadarray EBImage Cancer beadarray EBImage

updated 15.0 years ago • Mark Dunning

div class="preformatted">To whom this may concern:     I must first apologize for not being a bioinformaticist and really only "pretend" to know how to use R to analyze microarray...lt;- makeContrasts(x3Dvsinvivo = x3D - invivo, + x3Dvsx2D = x3D - x2D, + x2Dvsinvivo = x2D - invivo, levels = design) > fit2 <- contrasts.fit(fit, cont.matrix) &am…

Microarray affy limma Microarray affy limma

updated 16.4 years ago • Stephen V. Su

Warning messages: 1: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 2: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 3: In curl::curl_fetch_disk...url, x$path, handle = handle) : progress callback must return boolean 4: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress …

annotationhub

updated 10.1 years ago • acaugu

<div class="preformatted">Hi, I'm trying to normalize a table of probe level intensities (pls. see attachment). Would you recommend a method, which would take only a matrix but not an AffyBatch or object...div class="preformatted">Hi, I'm trying to normalize a table of probe level intensities (pls. see attachment). Would you recommend a method, which would take only a matrix but not …

Normalization probe Normalization probe

updated 15.4 years ago • dorothyc

these events have taken place within the boundaries of genes, and I would like to retrieve the gene names (ensemble ID). I've tried to use biomaRt: > getBM(attributes=c("ensembl_gene_id"),filter=c("chromosome_name","star t","end"), values

updated 15.9 years ago • Boel Brynedal

criteria to CRAN packages for submission. Can you recommend additional resources (where to start, validation tests...., for instance) for package development in Bioconductor? Kind regards, D

package R software development

updated 5.2 years ago • Dany

SYMBOL") Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'SYMBOL'. Please use the keys method to see a listing of valid arguments. ``` </numeric></numeric></numeric></numeric></numeric

RNASeq R

updated 4.6 years ago • Rishav

of green and yellow. The problem seems related to the > conversion of the categories to factor levels - in the absence of one > category there will always just be levels 1 and 2 and not e.g. 1 and 3. > thanks for the feedback...in the example you provide, since the default colours listed in the documentation are wrong. I must admit that this is something I never put much tho…

Category HTqPCR Category HTqPCR

updated 14.5 years ago • Heidi Dvinge

error:  Error in .normargGenome(value, seqnames(x)) :    supplied 'genome' must be a vector or factor  These were the steps I was running: library(Gviz) library(GenomicRanges) library(GenomicFeatures...lt;- c(0, a$end) dtrack <- DataTrack(data = c, start = bed\_file1$start, end = bed\_file1$end, name = "Peaks (+)") dtrack1 <…

Gviz plot chipseq

updated 8.2 years ago • anupriyaverma1408

Hi all, I'm currently working with 16S data from an experiment involving two different strains of mice, at 4 different time points between P17 and P84. I'm attempting to analyze the differentially abundant taxa between genotypes at each postnatal age sampled. In addition, I'm hoping to make use of some previously acquired metabolite data to extract some differentially abundant taxa using SCFA …

deseq2 microbiome R

updated 5.2 years ago • greenm11

Error in stop("need data package: ", annlib) : object "annlib" not found Error in get(paste(lib, name, sep = ""), mode = "environment"): variable "hugene10stv1ENTREZID" of mode "environment" was not found Error in get(paste(lib, name, sep...was not found Error in dim(data) <- dim : attempt to set an attribute on NULL Error in names(x)<-value : 'names' attribute[3] must be same l…

oneChannelGUI oneChannelGUI

updated 17.5 years ago • Steve Taylor

readCtData(files="combined_file.txt", n.features=768, n.data=24, ...) Obviously, the your file names can be called whatever you want them to; these are just examples for simplicity. > - Each .txt must have miRNA name and Ct...or failed the quality control) etc. > - Moreover .txt for each sample I need a .txt with samples names and group?? > You'll need some sort of mapping…

miRNA qPCR PROcess HTqPCR miRNA qPCR PROcess HTqPCR

updated 13.4 years ago • Heidi Dvinge

header = TRUE) samples files <- file.path(dir, "results", samples$run, "quant.sf") names(files) <- paste0("sample", 1:10) all(file.exists(files)) txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene k <- keys(txdb, keytype...TRUE) txi <- tximport(files, type = "salmon", tx2gene = tx2gene, ignoreAfterBar = TRUE) …

RNA-seq Salmon tximport

updated 6.3 years ago • woojoy14

If I would like to represent a protein sub-network, what is the best data structure for it? It has the flat file format:   <table align="center" border="1" cellpadding="1" cellspacing="1" style="width:25%"> <tbody> <tr> <td><strong>Hub</strong></td> <td><strong>Interactor</strong></td> </tr> <tr> <td&…

AnnotationDbi Bimap Interactome

updated 7.6 years ago • Dario Strbenac

Hello! When I used dba.analyze() with my DBA object linking to bam files, I got errors. My command was as below. ``` anaScramblecst <- dba.analyze(Scramblecst) ``` It returned the errors *" No matching chromosomes found for file: ..bam" and "Blacklist error: Error in BamFile(file, character(0)): 'file' must be character(1) and not NA"* Then I tried ``` Scramblecstbl<-dba.blackli…

DiffBind

updated 4.9 years ago • ahua217

table from a gtf file, but am stuck. I do not have individual files from Salmon or other transcript level packages which is the input for tximport. Please help

tximport collapse

updated 6.4 years ago • agm

RE: Bioconductor Digest, Vol 68, Issue 23 Dear List, Is there an elegant way to obtain the name of a probe set from an Affymetrix platform (doesn't matter which one) corresponding to a given ENTREZ gene ID? It seems that...types: > -1, 1 and 0. 0 means normal probe; -1 mean negative control, i guess, and > the probe names are like (-)3xSLv1, NC1_00000002, etc[no corresponding pro…

aCGH Sequencing miRNA Microarray Annotation Normalization GO Preprocessing Visualization

updated 17.1 years ago • McGee, Monnie