Bioconductor Forum

dba(data, bSummarizedExperiment=TRUE) Error in FUN(X\[\[i\]\], ...) :   assay rownames() must be NULL or equal rowData rownames() / rowRanges   names() Any suggestions? &nbsp

DiffBind

updated 9.2 years ago • svohra

data.set),5,5))</pre> Results: <pre> > Treat [1] ctrl trtB trtA ctrl trtB trtA ctrl trtB trtA Levels: ctrl trtA trtB > Batch [1] 1 1 1 2 2 2 3 3 3 Levels: 1 2 3</pre> Design matrix: <pre> design <- model.matrix(~Batch+Treat) rownames(design...unsure is because this is the first time that I am using a treatment factor that has more than …

edger limma design matrix

updated 9.8 years ago • Ekarl2

to use DMRcate to analyze a large Illumina BeadChip 450k dataset. My phenotype variable has multiple levels: apart from the control samples we have samples from 8 different hematologic cancers. I construct my design matrix

dmr analysis dmrcate

updated 10.3 years ago • irini.liampa

talented workforce. EOE Disability/Vet/M/F/Sexual Orientation/Gender Identity. Staff at PNNL must be able to demonstrate the legal right to work in the United States. __Minimum Qualifications__ Candidates must have

proteomics machine learning git docker Job

updated 7.9 years ago • petyuk

div class="preformatted"> Hello, I am trying to convert a file of gene names to corresponding affy probe names. I managed to write a script that puts the genes in an array then I use the feat = getFeature...mart = mart) in biomaRt however I seem to hit a snag when there is more than probe for a gene name. Does anyone know of an existing script that can do this? thanks Ruppert ________________…

probe convert biomaRt probe convert biomaRt

updated 17.6 years ago • Ruppert Valentino

Hi, I was trying to make a list of SNPs and names of genes they are related to. So I used the VariantAnnotation package  <pre> locateVariants(target, TxDb.Hsapiens.UCSC.hg19.knownGene...error: <pre> Fehler in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to see a listing of valid arguments…

TxDb.Hsapiens.UCSC.hg19.knownGene org.hs.eg.db

updated 9.1 years ago • Lna

the following error message. I believe it might be at the estimateDispersions step. "Error in names(res) <- nms : 'names' attribute [16] must be the same length as the vector [1] Calls: estimateDispersions ... estimateDispersions

software error

updated 5.4 years ago • huck.thornton

a .csv file as an input, but keep getting the error: | | | 0% | |=========== | 22%Error in names(comp)\[1\] <- "value" : 'names' attribute \[1\] must be the same length as the vector \[0\]< I am following the formatting that is given

PAPi

updated 8.8 years ago • k_hulce

To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Subject: [BioC] multi-level design - a simplified question - corrected > table > > Hello all, > > I do need some help on analyzing such unorganized...data. Please help me out. Thank you so much! > I basically followed the analysis of multi-level experiments in l…

updated 11.3 years ago • Gordon Smyth

coldata),collapse="+") covariate=as.factor(covariate) > covariate \[1\] condition+batch Levels: condition+batch dds <- DESeqDataSetFromMatrix(countData = cts1,colData = coldata,design = ~ __covariate__) I am getting...below error. It is not taking column names from covariate object. Am I doing wrongly.  __Error in DESeqDataSet(se, design = design, ignoreRank) :&a…

deseq2 design matrix

updated 7.6 years ago • vrehaman

Dear All, I have chromatin data, from ATAC and other histone marks and RNA-Seq data for same samples. Lets say I have 14 independent samples subjected to ATAC-Seq and RNA-Seq, but at different times, different sequencing centres. Now I want to compare the signal from chromatin data to gene expression data, lets say calculating the correlation values of chromatin signal at a peak to near by gene…

atac-seq atac deseq2 sva combat

updated 8.8 years ago • g.atla

fiveUTRs = fiveUTRsByTranscript(txdb, use.names = TRUE) names5UTR = names(fiveUTRs) cds = cdsBy(txdb, "tx", use.names=TRUE) namesCDS = names(cds) names5UTRCDS = intersect(namesCDS,names5UTR) fiveUTRs...for (i in 1:length(names5UTRCDS)){ x = GRangesList(c(unlist(fiveUTRs[i]),unlist(cds[i]))) names(x) = names(fiveUTRs[i]) fiveUTRCDS = c(fiveUTR…

annotation concatenation GRangesList GenomicRanges

updated 6.7 years ago • anmej

<div class="preformatted">Hi everybody. I am currently using rtracklayer a lot, but I am experiencing some problems with the names of the trackas and tables. For example, I wanted to query the NKI Lads track, which is a hg18 liftover available from the UCSC browser. I do the following: > s <- browserSession() > genome(s) <- 'hg19' > tn <- track…

rtracklayer rtracklayer

updated 12.8 years ago • Gustavo Fernández Bayón

and counts) and was wondering if there is a better way to read my individual counts data so the path name does not show as a sample name. It is starting to get annoying and I am afraid it will mess with downstream analysis. Below

edgeR

updated 22 months ago • aa.machado001

Hi, I need transcript or isoform level counts. I tried gene level first. The result of GAPDH gene looks good: `` ENSG00000111640.14 35281 44063 44933 37448 41543...nthreads=16, strandSpecific=2</pre> I then tried some parameter combinations of for transcript level. All combinations produced very low (<100) counts for GAPDH except that one trial created high TOTAL counts (part): &l…

rsubread

updated 9.8 years ago • Likai Mao

<div class="preformatted">hi members, is there any function or easy way to get the gene level of a human exon affymetrix chip? currently i calculate the average of all exonic probeset intensities for genes of interest...div class="preformatted">hi members, is there any function or easy way to get the gene level of a human exon affymetrix chip? currently i calculate the average of all e…

updated 17.6 years ago • Paul Hammer

PCR? >Is it okay to publish pathway overrepresentation >analyses with this cutoff, or is PCR validation of the cutoff >advised? > >Thanks and best wishes, >Rich >------------------------------------------------------------ >Richard A. Friedman, PhD >Associate Research...on journal policy and isn't for us to say. But, generally speakin…

Network Cancer limma Network Cancer limma

updated 19.7 years ago • Gordon Smyth

the waterfall plot using the package but I would like to get the mutation frequency data by gene name (the subplot of % Mutant against gene name plotted using waterfall function in GenVisR) in table for analysis. Welcome any

GenVisR mutation frequency R cancer bioconductor

updated 6.2 years ago • sheneicechang

<div class="preformatted">Dear all, I just received a message from Philips Research for a post doc position. Maybe somebody is searching for a new job challenge. *Science jobs from Philips Research * *Field of Research: prostate cancer, functional biomarker validation, gene expression, imaging, tumor models, functional assays Host: Philips Research, Eindhoven, the Netherlands Duration...…

Cancer Prostate Cancer Prostate

updated 16.4 years ago • Paul Hammer

package to plot pathways with moderate success. When I am working with ~100 nodes, the gene names are included on my final plot. However, when I have larger datasets (~300 nodes) the names disappear. I am using the same method...to obtain gene names and the same parameters to add them to the plots. Does anyone know how to solve this? ```r ##Plot parameters nA <- makeNodeAttrs

KEGGgraph

updated 2.5 years ago • hilarius_bookbinder

set operations (union, intersect, setdiff) on DNAStringSets, but doing so strips off the names. How can I do set operations while keeping the names intact

biostrings

updated 9.5 years ago • nicholasbauer

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updated 18.4 years ago • carol white

I am working on affy microarray CEL file: GSM4445975 I know we can extract probe level intensity by using: but can I still access to the probe level intensity after the rma() ? ```r head(exprs(data.raw)[probe_table

MicroarrayData AffymetrixChip

updated 3.6 years ago • Haoran

normalizeBetweenArrays(E, method="quantile") I don't understand you question about getting gene names in the toptable, as this should happen automatically. Best wishes Gordon > Date: Fri, 27 Aug 2010 10:59:10 -0700 > From: "Orfe...hoping that some of the experts that read > these posts could comment on it - specifically, is it valid? Is there > something I could be…

Bayesian limma PROcess Bayesian limma PROcess

updated 15.3 years ago • Gordon Smyth

Hi. I am trying to make sense of a previously written DESeq analysis which uses the “name” parameter to obtain results. A sample code is below, the first two lines are straightforward - making the Input file and...Hi. I am trying to make sense of a previously written DESeq analysis which uses the “name” parameter to obtain results. A sample code is below, the first two lines are straightforward -…

deseq2 rnaseq

updated 8.1 years ago • muratcokol

<div class="preformatted">Hello all, I do need some help on analyzing such unorganized data. Please help me out. Thank you so much! I basically followed the analysis of multi-level experiments in limma user guide. But I do not feel right about the code below. Please give me some suggestions. # I want to compare Normal vs. Tumor negative, and Normal vs Tumor positive. There are partial pa…

updated 11.4 years ago • Rao,Xiayu

gt; hg19_tx <- extractTranscriptsFromGenome(Hsapiens, hg19txdb) #Create DNAStringSet with names associated with each probe > probeset <- DNAStringSet(probelist$sequence) > names(probeset)<-probelist$probenames...25 [3] 804 828 25 [4] 757 781 25 The result of matchPDict is a MIndex object that I named txmatches with exact matches, and txmatches1 wit…

probe probe

updated 14.3 years ago • Ian Henry

frame dim(df)= 29 20664. It contains mutation and copy number variation data for genes. The column names are actually gene names. The column names currently are gene1, gene2 .... gene20664. __How can I change the column...names from 1 to 19862 as gene1\_mut, gene2\_mut ... gene19862\_mut __ __and from 19863 to 20664 as gene19863\_CNV, gene19864..._CNV..... gene20664\_…

annotation

updated 10.0 years ago • qurrat.ulain

rowData(vcf) loc <- locateVariants(target, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, AllVariants()) names(loc) <- NULL out <- as.data.frame(loc) </pre> Is there anyway to have, for each variant, the sample or samples that have that

annotation variantannotation sample

updated 10.5 years ago • by0

r permut <- model.matrix(~ 0 + aerobicity + timing) ``` And this yields the following, dropping level T0, which makes sense. ```r aerobic anaerobic T1 T2 T3 1 1 0 0 0 0 2 1 0 0 0 0 3 1 0 1 0 0 4 1 0 1 0 0 5 1 0 0 1 0 6 1 0 0 1 0 7 1 0 0 0 1 8 1 0…

edgeR RNASeq

updated 4.7 years ago • Ryan

to load in the preinstalled data but when i try my own i get the error Error in split.default(names(sort(nl)), f.index): first argument must be a vector I have found some similar post/problems but i still cannot identify the...extract the adjusted p-values from our results object geneList <- res$padj # add the gene names from our results to our list of adjusted p-values names(…

topGO GO

updated 3.0 years ago • peter

the following design: <pre> ~ patientID + treatment</pre> (where patientID is a factor with 39 levels indicating the paires and treatment  is a factor with 2 levels: baseline/post treatment).  This design works...are known to influence gene expression in humans, i.e. age (numeric), smoking status (factor with 2 levels: current smoking/ non smoking) and gender (fa…

deseq2 deseq paired samples covariates multiple time points

updated 8.2 years ago • imb

I am now hesitant to use lfcShrink on this comparison, as I cannot use the coef() argument. Is it valid, to just use the contrast argument as I did it in the results? Here is the code ```r design2 <- as.formula(~cell_group) modelMatrix2...These are my two desired comparisons rDC3vDC2_c<-results(ddsObj2, name="cell_group_DC3_ctrl_vs_DC2_ctrl", …

lfcshrink R DESeq2

updated 3.6 years ago • LHA_trash

the intensity > size = ncol(affy.data) > IN = intensity(affy.data) > > #get the celfile names > cels = colnames(IN) > #put the prefix to the celfile names > newcels = paste(prefix,cels,sep="-") > #get the number of chips &gt...go through each chip and write the new celfile for it > for( i in 1:col.count){ + #old celfile name for t…

cdf affy affxparser cdf affy affxparser

updated 15.8 years ago • Guido Hooiveld

<div class="preformatted">Hello everyone, I am currently working on GLM for RNA-seq data in DESeq for a design with two factors and three factor levels, such as: type experiments A_1 A exper1 A_2 A exper2 A_3 A exper3 B_1 B exper2 B_2 B exper3 B_3 B exper4 C_1 C exper4 C_2 C...am currently working on GLM for RNA-seq data in DESeq for a design with two factors and three factor levels, such…

DESeq DESeq

updated 13.0 years ago • Dorota Herman

design model in DESeq2 for the following experiment: Basically I have a condition factor with three levels: Control, Asymptomatic, Symptomatic. It is clear how I'll perform the simple analysis for differentially expressed...p/104783/ And as I now realised I can simply do the tilde condition design with three levels and then do <pre> results(dds, contrast=c("condition","symptomatic","as…

deseq2 model design differential gene expression experimental design

updated 7.9 years ago • L_K

Hi, I'm working with .cel-files and after applying RankMerging function I loose my sample names. >eset <- justRMA(filenames = list.celfiles(path=celpath, full.names=TRUE)) >MergingSet <- RankMerging(eset ,"Spearman...eset ExpressionSet (storageMode: lockedEnvironment) assayData: 22277 features, 3 samples element names: exprs, se.exprs protocolData sampleNames: chr…

GO GO

updated 11.4 years ago • Guest User

another one I could see the following lines whcih I am unable to understand. In range 1: 'end' must be >= 'start' - 1.: .Call2(\"solve_user_SEW0\", start, end, width, PACKAGE = \"IRanges\")" Please check and let me know if I could provide any

Genomicranges IRanges

updated 6.1 years ago • bioinagesh

geneList<-factor(as.integer(probekeys %in% intgenes) # intgenes= my list of interesting probeIDs names(geneList)<-probekeys str(geneList) Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ... - attr(*, "names")= chr [1:33295] "7892501" "7892502" "7892503" "7892504...object ------------------------- test.stat <- new("classicCount", testStatistic = GOFisherTest, name = "Fisher t…

GO graph GO graph

updated 12.7 years ago • Guest User

error when plotting the heatmap:  `` Error in cutree(tree, cutree_n) : elements of 'k' must be between 1 and 3 ``.  I cannot figure out what k is (I thought the number of cluster to be formed, but why does this need to

R monocle

updated 8.4 years ago • A.H

45PM +0100, Crispin Miller wrote: > > Hi, > > Just a quick question about low expression levels on Affy systems - I > hope it's not too off-topic; it is about normalisation and data analysis... > > I've heard a lot of people...gt; an initial filtering on either Present Marginal or Absent calls, or on > gene-expression levels (so that only ge…

affy affy

updated 22.5 years ago • Gordon Smyth

embedded message was scrubbed... From: Paul Hammer <paul.hammer@p-t-p.de> Subject: Re: [BioC] gene level on exon chip? Date: Thu, 17 Apr 2008 16:56:37 +0200 Size: 3096 Url: https://stat.ethz.ch/pipermail/bioconductor/attachments

updated 17.6 years ago • Paul Hammer

then get the following error.</span> <pre> Error in if (any(input.mean < 0)) stop("input.mean must be non-negative") : missing value where TRUE/FALSE needed Calls: estimateCommonDisp -> equalizeLibSizes -> q2qnbinom

edger

updated 10.4 years ago • bastian.hornung

FALSE, + indicate = c("condition", "replicate"),plot=TRUE) Error in names(cols) <- var : 'names' attribute [7] must be the same length as the vector [2] I have used the same data for generating pca plot and

dep

updated 5.5 years ago • nkvnambiar

Error in .validate_names(rownames, ans_rownames, "assay rownames()", "rowData rownames() / rowRanges names()") : assay rownames() must be NULL or identical to rowData rownames() / rowRanges names() ``` I found that it has to do with "SummarizedExperiment

soggi

updated 6.7 years ago • nicolas.descostes

number of genes=31099 annotation=rat2302 notes= > QCReport(affy.batch.sub) Error in attr(groups, "names") <- names : 'names' attribute [16] must be the same length as the vector [1] Enter a frame number, or 0 to exit 1: QCReport(affy.batch.sub...2: signalDist(object) 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = "Array 4: boxplot.default(object, names…

affy affy

updated 18.4 years ago • Mark W Kimpel

What is the difference in annotation between the bioconductor packages pd.hugene.2.1.st and hugene21sttranscriptcluster.db? I have affymetrix data (hugene 2.1.st (sense target) 16-Array Plate). Before annotation, I performed RMA-preprocessing, which includes RMA-background correction + quantile-normalization + summarization (target = core) using the bioconductor package oligo (bioconductor versi…

annotation microarray bioconductor pd.hugene.2.1.st hugene21sttranscriptcluster.db

updated 7.2 years ago • Irene

expression analysis comparing multiple groups at the same time. My sampleTable is the following: Name Condition Differentiation AF_MSCs_1 AF_MSCs_1 AF_MSCs low AF_MSCs_2 AF_MSCs_2 AF_MSCs low AF_MSCs_3 AF_MSCs_3...analysis to identify differentially expressed genes in the condition taking into account the level of differentiation. I got the following message. dds &…

deseq2

updated 5.6 years ago • dequattro.concetta

to write.table) to write expression data to a text file, the output text file has one less column name (the probe ID column does not get a name), and the other column names are shifted all the way to the left margin in the text file...may be a little off here, depending on the display font, but here you can see that the probeset name is the row label) 6187.CEL 6188.CEL 6189.CEL 6190.CEL…

probe limma probe limma

updated 20.8 years ago • Ken Termiso

failed in loadNamespace() for 'httr', details: call: options() error: Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'NULL' sessionInfo(R-4.1.0

PackageLoading

updated 4.1 years ago • dozhun

genes for organism 'human' in GO database -> filtering GO terms according to evidence levels 'all' -> loading files with information content for corresponding GO category (human) finished. -> retrieving GO information...genes for organism 'Homo sapiens' in GO database -> filtering GO terms according to evidence levels 'all' calculating diffusion kerne…

go.db software error bug

updated 10.6 years ago • lejeczek

fit[,-1], cont[-1,2]) `` `` lmfitebayes <- eBayes(lmfit.cont) `` `` topTable(lmfitebayes, coef=name, number=Inf) `` Which fails when executing topTable sometimes. Thats because `` contrast.fit `` in some cases prefers not...to give a name to the coefficients (see below). It does not give the name if only a single contrast is being computed. If I than want...t…

limma

updated 8.0 years ago • wewolski

When using Rsubread v 1.28.1 it sucessfully parsed my input file names by removing the file path and just keeping the names. As of the current version, however, the names contain the entire file...path, this makes for very long and ugly column names. Example ---- Setup --- files: /path/to/file/here/file1.bam; /path/to/file/here/file2.bam countData=featureCounts(.....) ------- 1.28.…

Rsubread featureCounts

updated 6.6 years ago • wunderl

Hello, Referring the limma user guide section 9.7-Multi-level experiments (pages 49-50), This experiment involves 6 subjects, including 3 patients who have the disease and 3 normal...TissueAvsTissueB= (Diseased.A+Normal.A)/2 - (Normal.B+Diseased.B)/2, levels=design) ``` Yusuf

limma microarray affy

updated 6.0 years ago • cyusufd

<div class="preformatted"> I downloaded a number of SNP 500K data from GEO to run with CRLMMM. The following CEL files specified by GEO as NspI files. > fulFileNames [1] "/Users/pcoyne/B_Cluster_DBased/GSE9222/NspI/GSM234158.CEL" [2] "/Users/pcoyne/B_Cluster_DBased/GSE9222/NspI/GSM234160.CEL" [3] "/Users/pcoyne/B_Cluster_DBased/GSE9222/NspI/GSM234162.CEL" > crlmm (fulFile…

SNP crlmm SNP crlmm

updated 16.4 years ago • mcoyne@boninc.com

Hello. I am trying to remove the gene names from a heat map I generated because there are many genes, and the gene names on the right side of my heatmap do not correspond

DESeq2

updated 4.4 years ago • Emma

rowSums(counts(dds) >= 10) dds <- dds[keep, ] dds$Condition <- factor(dds$Condition, levels = c("Normal","Tumor")) res <- results(dds, name="Condition_Tumor_vs_Normal", alpha=0.05, lfcThreshold=0.58) resOrdered <- res...NA A2ML1 5.00733 0.0147204 1.32641 0 1 NA ``` All genes are named in this range: A1CF --> A…

DESeq DESeq2

updated 3.4 years ago • manwar

invisible() } <environment: namespace:base=""> and the tracebck > traceback() 7: stop("'by' must specify valid column(s)") 6: fix.by(by.x, x) 5: merge.data.frame(ndfdata, xysdata, by.x = c("X", "Y"), by.y = c("X", "Y")) 4: merge(ndfdata, xysdata, by.x...OK Parsing file: nobless1.xys... OK Merging NDF and XYS files... Erreur dans fix.by(by.x, x) : 'by' must specify valid colu…

BiocViews Microarray Annotation Organism biocViews BiocViews BiocViews Microarray Organism

updated 15.2 years ago • Michael MOZAR

Hi all, I am using TCGA level 3 data (rsem raw counts) for samples with matched normal to analyse differential expression using DESeq2. I was wondering

deseq2 tcga experimental design multiple factor design

updated 10.5 years ago • anand m t

them up iteratively as I process new data. What I've not been able to sort is how to define coulmn names after the dataset is created. It appears possible when you feed in a dataframe, but not a matrix. ```r # create a dataset using...I've been able to get it to work using the h5dfr package as an attribute so perhaps column names are using the h5writeAttribute? I haven't been able to sort the…

h5createDataset rhdf5

updated 2.8 years ago • kpalmer