Bioconductor Forum

In the bioconductor tutorial for gviz I have noticed that sometimes the name of a track disappears from the plot if the track is small. Is it possible to set the minum height of the track, so that the...name of the track does not disappear (is independent of the track height) ... or is it possible to set the minimum size of the legend

gviz

updated 10.7 years ago • tonja.r

dataset = dataset, mart = mart) : The given dataset: celegans_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function. > m <- useMart(biomart="ENSEMBL_MART_ENSEMBL...dataset = dataset, mart = mart) : The given dataset: celegans_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.…

biomaRt bioconductor celegans annotation

updated 7.9 years ago • clarisbaby

rqcResultSet)\`   I get the following error: Warning: Error in eval.quoted: envir must be either NULL, a list, or an environment. Stack trace (innermost first):     107: eval.quoted     106

software error bug library

updated 8.8 years ago • guus.steeg

like to get the number of up and down genes from my QLF test. Treatment <-factor(targets$treat,levels=c("Sham","Infected")) Strain <- factor (targets$strain, level=c("D","R")) y = DGEList(counts=x\[,1:8\]) keep <- rowSums(cpm(y)>1) >= 4 y <- y\[keep...qlf) summary(dt <- decideTestsDGE(qlf)) __Error in array(x, c(length(x), 1L), if (!is…

edger DGE coef

updated 8.1 years ago • rebeccajane93

file and would like to extract gene expression for further analysis. However, there is no name for the assay, how I can change the name or subset data. Thank you data class: SummarizedExperiment dim: 15093 100 metadata...rownames(15093): ENSG00000000003 ENSG00000000419 ... ENSG00000273488 ENSG00000273489 rowData names(3): Ensembl_ID GeneID EntrezID colnames(10…

deseq2

updated 5.4 years ago • georgina.fqw

reasons that I'm not sure I understand, the argument list used in the definition of this S4 method must start with 'x'. The consequence of all this is that dispatch will happen on 'x' so if named arguments are passed with a name that...length 0 > c(a=IRanges(), x=IRanges()) IRanges of length 0 But when all the arguments are named with names != 'x', then nothing is passed to 'x' and…

Cancer IRanges BiocGenerics Cancer IRanges BiocGenerics

updated 13.0 years ago • Hervé Pagès

different from Illumina's. I noticed that the 'beadarray' package has the ability to read in bead-level data, and while I'm sure this isn't the most scalable solution, given the way that Infinium arrays are structured, the thought...From the raw data, I constructed a 'targets' file (attached) and then attempted to pull in the bead-level information from a couple of arrays (so as not to exceed my…

Annotation Preprocessing Annotation Preprocessing

updated 16.4 years ago • Tim

div class="preformatted">Hi, suppose I have a list of gene names like below, is there a "fuzzy"-matching based algorithm to convert gene name to locuslink id's? > head(anno[,4]) [1] Comp Rheb Ctsj

convert convert

updated 18.5 years ago • Weiwei Shi

mart, dataset = dataset, verbose = verbose) : The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets function. human <- useMart(biomart = "ENSEMBL_MART_ENSEMBL...mart, dataset = dataset, verbose = verbose) : The given dataset: hsapiens_gene_ensembl, is not valid. Correct dataset names can be obtained with the listDatasets fun…

software error biomart ensembl

updated 9.5 years ago • genomicsio

1.38.3 >hg19db <- makeTxDbFromUCSC(genome = "hg19",tablename ="knownGene") Error in names(trackIds) <- sub("^ ", "", nms[nms != "new"]) : 'names' attribute [212] must be the same length as the vector [211] </pre>   Does anybody have the

maketxdbpackagefromucsc rtracklayer genomicfeatures

updated 7.4 years ago • lalchungnungabt17

I realized that I get different results for one factor dependent on the order of levels within another factor. In principle, I have 2 factors with 2 levels: Age (young, old), and Type (Treated, Control) I have performed...a DESeq2 model with ~ Age + Type + Age*Type When I use 'relevel' to change the order of the levels of the Age factor in the design matrix, I get different results for the T…

deseq2

updated 5.8 years ago • dfab

this: samples <- RangedDataList(RR05ranges,RR06ranges,RR2_03ranges,RR2_04ranges) Can i assign names like this? names(samples) <- c("RR05","RR06","RR2_03", "RR2_04") It works, but my worry is that the order might be different if objects...do not have a fixed order..... Or is there a way of assigning a name to each RangedData object before they are added to a list? Thank you! As …

htSeqTools ASSIGN htSeqTools ASSIGN

updated 13.9 years ago • Ian Donaldson

tbody> <tr> <td> <p> </p> </td> <td> <p>I´m using bioconductor and I want to extract the tissue name of the cel files (not the file name itself because a lot of cel files with different names can be related to the same tissue...in order to create a principal component analysis scatter plot where each group name is equals to tissues names. I do…

pca oligo cel

updated 10.4 years ago • angel.ruvalkba

<div class="preformatted">Sorry, I forgot to have a subject on the mail I sent before. Hello everyone. I would really appreciate some comments/hints/help with a pretty long question. I have an experiment consisting of 18 hybridizations. On the 30K cDNA arrays knee joint bioipsies (from different patients) before and after a certain treatment is hybridized. What I want to find out is the e…

limma limma

updated 21.7 years ago • Johan Lindberg

CEL files using: >data.test<-ReadAffy(widget=TRUE) So I would like to look at the first sample name of my data: >sampleNames(data.test[1]) [1] "C:/Program Files/R/rw1090/rdata/JS1999081101AA.CEL" Why are the sample names displayed

updated 21.6 years ago • Vitalina Komashko

from TCGA and now I'm trying to prepare the data with the function TCGAprepare, for probe-level microarrays is fine (if I put SummarizedExperiment as False, otherwise give me an error), but for the platforms of oligonucleotide

tcga tcgabiolinks microarray exons oligonucleotide

updated 9.6 years ago • Fernando

Error in validObject(.Object) : invalid class "GRanges" object: 'seqlevels(seqinfo(x))' and 'levels(seqnames(x))' are not identical Calls: do.call ... .unlist_list_of_GenomicRanges -> new -> initialize -> initialize -&gt

variantannotation seqlevels error

updated 11.2 years ago • Asma rabe

I have been asked to do a gene level expression analysis of an experiment that used Affymetrix GeneChip Mouse Exon 1.0 ST Arrays: http://www.ebi.ac.uk...I have been asked to do a gene level expression analysis of an experiment that used Affymetrix GeneChip Mouse Exon 1.0 ST Arrays: http://www.ebi.ac.uk/arrayexpress...package from CRAN, restricting to core probe-sets. We used to convert from exo…

affy aroma.affymetrix exon array xps oligo

updated 8.4 years ago • Gordon Smyth

pre> gff <- import('hsa.gff3') hairpin <- gff[mcols(gff)$type == 'miRNA_primary_transcript',] names(hairpin) <- mcols(hairpin)$ID mature <- gff[mcols(gff)$type == 'miRNA',] names(mature) <- mcols(mature)$Derives_from mature_relative...lt;- shift(mature, -start(hairpin[names(mature),])) names(mature_relative) <- mcols(mature)$ID</pre> Thi…

genomicranges

updated 10.0 years ago • Jake

Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData > Could you please help with it, Galina

BatchQC batchinDeseq2. columnsincolData.

updated 18 months ago • Galina

of my question properly. What I really meant is to compare : >>> >>> "Factor A level 1" vs "Factor A level 2" within "Fact B level 1" >>> "Factor A level 1" vs "Factor A level 2" within "Fact B level 2" >> >> I don...in the results of DESeq2 analysis really mean for the interaction of a two-factor …

Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2

updated 11.4 years ago • Shucong Li

I went through to your doc* and I searched a lot on ncbi, internet to find out what is the full name of these columns? You must have it somewhere, all serious scientific work always give the full names of the abbreviations...I went through to your doc* and I searched a lot on ncbi, internet to find out what is the full name of these columns? You must have it somewhere, all serious scientific wo…

ChAMP

updated 5.7 years ago • julie

science, bioinformatics, much less R and DESeq2. I am having issues with R removing the gene ID names in my countData. My raw countData appears as follows: ``` 2416X12 2416X13 2416X10 ENSOARG00000000001 0 0 0 ENSOARG00000000002...0 2 319 30 524 3 0 0 0 ``` As you can see, the gene names have been r…

DESeq2

updated 15 months ago • Olivia

  Hi all- I would like to be able to contrast the condition within a cell type (e.g. R1Vehicle vs. R1 Treated), but when I run DESeq with my group levels, it appears that the results from DESeq2 are already contrasting levels against a single level (P1Treated). Am I inputting the groupings wrong for my type and condition? Thanks in advance. <pre> a <- read.csv("~/Desktop…

deseq2

updated 8.0 years ago • Nmabe

error message when I was creating a flowSet consisting of two .lmd files.  <pre> Error in names(from) <- paste("V", seq(1, length(from)), sep = "") : 'names' attribute [2] must be the same length as the vector [0] </pre> My entire workscreen...0' as default. > x flowFrame object 'JennyG4a23052015.LMD' with 50000 cells and 6 observables: name …

lapply

updated 10.0 years ago • Wilson Yeo

the tximport pipleine for RSEM like following but when I checked the rownames, it gave me gene names instead of transcript names  <pre> rsem.files=list.files(".","*.isoforms.result") txi.rsem=tximport(rsem.files, type

tximport rsem

updated 8.2 years ago • deena

Would greatly appreciate if someone could clear this up for mem and confirm whether I would need validation from the normalized counts to confirm what I see on the log2FC level. Cheers

RNASeqData DESeq2

updated 2.3 years ago • Marina

total reads of a library). I think this is to be expected given the relatively low expression levels of lncRNA genes. Now this really affects the AveLogCPM values and the low-count filtering using the cpm() function of...edgeR. Is this way of read counting using the lncRNA subset a valid approach (statistically speaking)? This really greatly affects p-values and logCPM. How could I adjust low-…

edger rnaseq

updated 7.6 years ago • martin.weihrauch

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updated 17.9 years ago • Yuan Jian

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updated 18.3 years ago • Michaela Gündel

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updated 19.2 years ago • Noah Cohen

of affy vignete and ?ReadAffy) indicates that I need to set up a character array with both the file-names and the desired sample- names. This is what I have used (limited data-set for testing): > samples.files <- c( "RAE230A_043003_IM01T_LH.CEL...the purpose of the sampleNames argument? Or ss there another way of changing the "column" names in an eSet and in write.exprs()…

affy affy

updated 22.4 years ago • Paul Boutros

think this is perhaps because useDataset() does not expect Ensembl datasets to have spaces in their names, but some do. I have typed the following to try to select the Mycobacterium ulcerans dataset from the Ensembl Bacteria...lt;- useMart("bacterial_mart_9") listDatasets(ensemblbacteria) This tells me that the name of the Mycobacterium ulcerans data set is "EB 1 m_ulcerans". However, when I…

biomaRt biomaRt

updated 14.5 years ago • Coghlan, Avril

Ref ID and I want to get the rs# for these SNPs, is there an R package that can help me find the SNP name for each corresponding SNPRefID. I am  using SNPlocs.Hsapiens.dbSNP.20080617 package to find the SNP locations

SNP Homo sapiens SNPlocs SNP Homo sapiens SNPlocs

updated 16.5 years ago • Kay Jaja

nopackage" option exists, nonetheless I want to be sure that I cannot use any of the preexisting cdf names before using that one. The product used was **Infinium Global Diversity Array-8 (GDA) BeadChip by Illumina**. Any help would...be greatly appreciated as this is my first time using this package. As a reminder, these are the valid cdf names under crlmm: "genomewidesnp6" "genomewidesnp5"…

globaldiversityarray cdf crlmm

updated 20 months ago • mayra.haedo

div class="preformatted">I notice that edges appear to be named in two different ways: > edgeNames (g) [1:2] [1] "1~2" "1~3" > names (edgeData (g)) [1:2] [1] "1|2" "1|3" Does this different choice for separator character

updated 14.9 years ago • Paul Shannon

Hi Michael,     I'd like to ask a question related to a previous post: "Question: DESeq2 - factor base level changes the DE genes."     I ran the following code on DESeq2 (version 1.4.5): \#\# START CODE sampleTable <- read.delim(sample.table.file, row.names=1, stringsAsFactors=FALSE) coldata <- DataFrame(sample=sampleTable$SampleName, &…

deseq2

updated 10.2 years ago • Victor Missirian

inputFilePath, format = "fasta", findgRNAs = TRUE,  :    Please enter a name for the gRNA ouput file name! Could you please advise as to how I name the gRNA output file as I am unable to do this. Thanks

CRISPRseek OutputFileName

updated 9.1 years ago • bhanson1806

I am using DESeq2 1.10.1. I am facing model matrix error with "Levels or combinations of levels without any samples have resulted in  column(s) of zeros in the model matrix". From the manual

deseq2

updated 9.8 years ago • Raj

gt; > my.df = data.frame( start=my.starts, end=my.ends, space=my.spaces, strand=my.strands, name=my.names, delta=my.delta ) > my.rd = as( my.df, 'RangedData' ) > my.gr = as( my.rd, 'GRanges' ) > # Extract the name field from each of...these objects using [[ > print( my.df[[ 'name' ]] ) [1] seq1 seq2 seq3 Levels: seq1 seq2 seq3 > print( my.rd[[ 'name' ]]…

IRanges IRanges

updated 15.3 years ago • Tim Yates

div class="preformatted">I am looking for a way to convert geneid to gene name. Specifically, I am calling for variants and then using VariantAnnotation to output using a predictCoding() function...CONSEQUENCE" "REFCODON" "VARCODON" "REFAA" "VARAA". I am interested in gene name moreso than GENEID and so I have been looking at how to do this including using the biomaRt p…

VariantAnnotation convert biomaRt VariantAnnotation VariantAnnotation convert biomaRt

updated 12.9 years ago • Matthew Liebers

plotBCV which has a legend included in the top-right corner of the plot. I would like to change the names in the legend because when I reduce the size of the plot to export it to pdf, the names in the legend goes out of the box. I tried

edger plot Tutorial

updated 7.3 years ago • Juan

files, importer, geneIdCol, abundanceCol, : all(c(geneIdCol, abundanceCol, lengthCol) %in% names(raw)) is not TRUE In addition: Warning message: Unnamed `col\_types` should have the same length as `col\_names`. Using smaller...way? * If using only one file, should I us eit in a diff way? * Maybe the file must be zipped? * Maybe it must have this suffix: "genes.…

tximport RSEM import error

updated 5.3 years ago • harelarik

as follows: ``` > exprs_mainProbes<-getMainProbes(exprsgs, pd.hta.2.0) Error in switch(level, core = dbGetQuery(con, paste("select distinct core_mps.transcript_cluster_id, type from featureSet inner join core_mps...EXPR must be a length 1 vector ``` Could you shed light into this problem? Thanks in advance

annotation affy

updated 6.6 years ago • a.karanikolou

I want to use the groupGO function from cluster profiler, but do not exactly understand the `` level `` argument. The help page (hence `` ?groupGO) `` says: "Specific GO level." When I play around with it (giving it different numbers), I...ont = "BP", level = 2, readable = F) > dim(as.data.frame(ggo_all)) [1] 33 5 > ggo_all <- groupGO(gene = All_genes, keytype = "ENSEMBL"…

clusterprofiler go groupGO

updated 7.6 years ago • b.nota

package is all about? Like the theory/rationale behind it and why/how it is better than rma? I must be doing something wrong, but my rma expression levels are the same as what I got from gcrma. Granted I just ran: data <- ReadAffy...eset.rma <- rma(data) eset.gcrma <- gcrma(data) But the expression levels generated were identical. I didn't believe it, so I'm re-running th…

gcrma gcrma

updated 22.0 years ago • Stan Smiley

class="preformatted">Hi! We want to classify a new type of glands by ranking genes by expression level using RNAseq. We don't have any good controls, so we just want to see a ranked list of genes. I have used Cufflinks RPKM values...but if I want to use edgeR, is this a valid way of doing it using featureCounts: fc <- featureCounts(files=targets$Targets,nthreads=8, isGTFAnnotationFil…

RNASeq edgeR RNASeq edgeR

updated 11.6 years ago • Sindre

quehist1[['AH29884']]` line). The error printed was: Error: failed to load resource name: AH29884 title: E003-H3K4me3.narrowPeak.gz reason: 1 resources failed to download 9.stop("failed to load resource", "\n...name: ", names(x), "\n title: ", x$title, "\n reason: ", conditionMessage(err), call. = FALSE) 8.value[[3L]](cond) 7.tryCatchOne(expr, names, parentenv...2.quehist…

AnnotationHub

updated 5.3 years ago • ben.ponv

I have RNA-seq data from a 3-level 1-factorial experiment: non-treated control, placebo-treated negative control, and treated cells. I have 3 replicates...for each. After running edgeR, and also looking at expression levels, I noticed that the negative control is not a good control, as it has DE genes compared to non-treated, while the treatment...is not DE for these genes (has the same…

edger limma model.matrix contrast matrix design matrix

updated 9.4 years ago • Peter

1. I am trying to add gene names to my result table from DESeq2 using the mapIds functions as outlined in the tutorial for differential analysis of...However I get the message:  " could not find funtion "mapIds""   How do I add gene names to my table?   2. Is there a way to add the gene names to the dds generated using the DESeq2 function:  dds = DESeqDat…

deseq2

updated 10.3 years ago • mtsompana

for every conversion. Is anybody aware of an R-package or script which supports "offline" gene name conversion, i.e. based on previously downloaded gene name database files (disk space is no problem)? Many thanks, Rainer

biomaRt DAVIDQuery biomaRt DAVIDQuery

updated 15.9 years ago • Rainer Tischler

very much for the valuable feedback! Yes, the function expects peak.ranges to be a RangedData with a "names" field as the name of the binding site. I will add your fix to make sure the function works when "names" field is not set. Thanks...space(myPeakList)), > start(myPeakList), end(myPeakList)) > colnames(z1) = c("name", "chr", "peakStart", "peakEnd") > &a…

ChIPSeq chipseq ChIPSeq chipseq

updated 15.9 years ago • Julie Zhu

of translated transcripts that contain the amino acid patterns I am interested in. Here are their names:> names(cds_seqs[i]) [1] "uc001ack.2" "uc001acv.3" "uc001adm.3" "uc001ado.3" "uc001adp.3" "uc001adq.3" "uc001adr.3" "uc001aee.1...uc009vle.1" "uc001ajj.1" "uc001ajk.1" [19] "uc001ajy.2" The question now is how do I go from these names to conventional protein names and (or) ENTREZ id…

GO GO

updated 13.6 years ago • Zybaylov, Boris L

within groups" followed by this: (in order to deal with the unbalanced nature of the experiment) "Levels without samples" I am getting stuck and don't know how to fix it ``` dsq <- phyloseq_to_deseq2(taxa_subset, ~ 1) > dsq class...version assays(1): counts rownames(52): Otu00001 Otu00002 ... Otu19614 Otu32323 rowData names(0): colnames(20): BP…

DESeq2

updated 22 months ago • DS

MC-0-1_GL0117883, LUJU01000040.1.orf00130, 2-1_GL0024467, I need to convert those name, to protein names that I can understand! Is there any package that I could use to convert these names? Please any help will

annotation

updated 5.2 years ago • mercedes.davalos-salas

Hi all, I'm looking for some help when analysing RNA-Seq data for differential exon usage/splicing. I've previously used edgeR for DE analysis and was happy to see diffSpliceDGE as part of that package. What I don't know is: 1. how to obtain exon level counts 2. whether there is a normalisation step involved like there is in a DGE pipeline (i.e. TMM) For the first point, I have...happy …

edger normalization differential exon usage splicing

updated 5.1 years ago • oakhamwolf

the number of samples that are present in each file." Samples are 4 "n.features*n.data must correspond to the total number of lines to be read from each file. " 8*4=32 But I have 96 lines of data? Do I have to make each technical...own feature? How then would I indicate that they are replicates if they each have their own feature name? I can't reuse feature names because I ca…

HTqPCR

updated 2.2 years ago • Ed Siefker

<div class="preformatted">I have been having an on-going discussion with a colleague about whether he can say that some genes are "absent" in some tissues based on two-color microarrays - most recently, Agilent arrays. There are a number of reasons that he would like to do this which are a mix of biology and QC. He wants to use some (arbitrary) normalized expression level, or unnormalized…

Sequencing Sequencing

updated 16.9 years ago • Naomi Altman

slot is empty) but calling new('AnnotatedDataFrame') produces an error where 'varMetaData' is not a valid slot name. Best. J. </div

updated 13.8 years ago • James F. Reid

<div class="preformatted">Dear Bioconductors, Now my problem is as follows: First of all, I read the microarray .gpr files to RGlist, then normalized it to MAlist. After that I convert the MAlist to exprSet for further analysis. Now, I want to filter genes in exprSet according to the names or probeID, but I found there is no geneNames Slot for my exprSet. How to find or keep the geneNames …

Microarray convert Microarray convert

updated 19.2 years ago • yanju@liacs.nl