Bioconductor Forum

of question, I get this: Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed when run: source("http://bioconductor.org/biocLite.R") on one RHEL 6.3 two other R version

updated 12.0 years ago • Pawel Eljasz

I'm trying to summarize an MSnSet object from PSM-level to peptide-level, and then to protein-level. I do this in two steps because I want to normalize on the peptide level. However, doing so <pre> pepqnt <- combineFeatures(qnt, groupBy = fData(qnt)$sequence, fun = sum) pepqnt_S <- normalise(pepqnt, "sum") pepqnt_norm <- normalise(pepqnt_S, "quantiles.robust") pro…

msnbase duplicate rforproteomics

updated 7.1 years ago • joris.vanhoutven

Hi, I am trying to get gene list using `` geneList `` function from `` refGenome ``. However, I got the following error.  best, ilyas. <pre> >library("refGenome") Loading required package: doBy Loading required package: RSQLite Loading required package: DBI > ens <- ensemblGenome() > cdir <- getwd() > basedir(ens) <- cdir…

refGenome geneList

updated 8.6 years ago • Mehmet Ilyas Cosacak

for starting the analysis, I get this error: ``` Error in `.rowNamesDF<-`(x, value = value) :duplicate 'row.names' are not allowed ``` even if online I found other posts with this problem, the solutions did not help me. When...I also get a warning message ``` In addition: Warning message: non-unique values when setting 'row.names': ‘0’, ‘1’, ‘10’, ‘100’, ‘101’, ‘102’, ‘103’, …

deseq2 rownames

updated 4.7 years ago • corellig

However, I was returned the error message: Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique value when setting 'row.names': ‘.’ Do you have any

software error

updated 5.1 years ago • lxiao63

Hi, I'm analyzing label-free proteomics data with DEP, but have run into an error of having duplicate row names. Here's what I have done: I have generated unique identifiers as indicated in the DEP tutorial: ``` > head(data...Hi, I'm analyzing label-free proteomics data with DEP, but have run into an error of having duplicate row names. Here's what I have done: I have gen…

DEP

updated 3.9 years ago • hele7

this error with the additional warning message: ``` Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values when setting 'row.names': ‘0’, ‘0.0011’, ‘0.0012...design = ~status, tidy = T) ``` My initial data contained duplicate row names; therefore, I tried to remove them by using make.names. After that…

DESeq2

updated 2.4 years ago • keremozdel9

ve been hitting a problem in this part: > pasillaCountTable = read.table( datafile, header=TRUE, row.names=1 ) > head( pasillaCountTable ) For my data, I have GeneID duplicates and consequently row duplicates. Anyone know

deseq2 genetics Tutorial

updated 6.9 years ago • anokhi1997

Hi all, My data is a data frame of estimated TPM counts, where rows are the genes and columns are the samples. I'm using "library(biomaRt)" to get ensembl symbols and hgnc symbols. When trying to change the rownames from enemble to hgnc symbols I get an error which stems from duplicates in hgnc symbols the way I understand it. The error I get: > "Error in `.rowNamesDF<-`…

r biomart genemap TPM

updated 4.6 years ago • Matan G.

up when an ExpressionSet object is intended to be created parsing a matrix expression data with duplicate row names: > try(myExpressionSet <- new("ExpressionSet", exprs = myexprsunique, phenoData = myphenoData, annotation...myannotation, check.names=FALSE)) Error in data.frame(numeric(n), row.names = nms) : duplicate row.names: blu I was wondering if there exists a way to crea…

Annotation Annotation

updated 13.4 years ago • nqueralt@clinic.ub.es

counts = Data , group = groups ) At this point, it keeps on giving me this error message: Error in \`row.names<-.data.frame\`(\`\*tmp\*\`, value = c("ML1,ML32,ML4,ML29,etc",  :   duplicate 'row.names' are not allowed non-unique values...when setting 'row.names':  But I know for sure that my row names are unique!  Any advice would be appreciated.…

edgeR row.names DGEList

updated 10.1 years ago • ccheung

exprs = myexprs, phenoData = myphenoData, annotation = myannotation) Error in data.frame(numeric(n), row.names = nms) : duplicate row.names: 1368290_at, 1368303_at, 1388202_at I'd like to fix that in an automated way in order to avoid...the script abortion. Does anyone know how to detect and eliminate duplicate rows in an expression matrix in an automated way? Best regards, Núria …

Annotation Annotation

updated 14.0 years ago • nqueralt@clinic.ub.es

could contribute to the 1h treatment of the first batch/study. also in the first study they have duplicates and in the second they have triplicates. I end up with the folliowing error: "Error in `.rowNamesDF<-`(x, value = value...invalid 'row.names' length Calls: rownames<- ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<-" I tried to…

DESeq2

updated 4.3 years ago • NGS_enthusiast

Hi, I am trying to annotate CpG calls ( a methylkit object). meth_gr has CpG calls coerced into GRanges. gene_bodies_hg38 has the gene body information extracted from a TXDB object made with Gencode 39 GTF. I have used the findOverlaps function to find the matches between "gene_bodies_hg38" and "meth_gr" and coerce them into a data frame. My code is provided sequentially below: > ma…

GenomicRanges methylKit S4Vectors

updated 3.0 years ago • hasche

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updated 18.7 years ago • Andre

Working with a workflow that uses Fastp -> Salmon -> Deseq2 Is it generally considered good practice to control for Fastp's read duplication rate and/or Salmon's percent mapped (from meta_info.json) when doing a Deseq DE analysis? I have noticed a fair amount...gt; Salmon -> Deseq2 Is it generally considered good practice to control for Fastp's read duplication rate an…

deseq2 salmon fastp

updated 5.5 years ago • rbutler

a set of Affymetrix arrays, all of the same type, among which there is for each sample a biological duplicate. I was wondering when I should "group" the duplicates : before normalizing ? After ? I can't either find how to do it properly

updated 16.0 years ago • ab19@sanger.ac.uk

Dear BioConductor list: I have a set of one color (cy3) data in which each gene was spotted duplicate in separate blocks (grids). I looked at how well the duplicated genes were correlated by using either "duplicateCorrelation...limma) or regular "Pearson" correlation test. Both tests gave out similar values around 0.55. Duplicate spots should be highly correlated in intensities. The correlation…

Normalization vsn limma PROcess Normalization vsn limma PROcess

updated 19.1 years ago • Jianping Jin

function, but that doesn't seem to apply. If I understand correctly, it's for averaging duplicate spots per probe, not duplicate probes per gene. It requires the same number of duplicates across the chip anyway

hgu133plus2 probe limma hgu133plus2 probe limma

updated 13.0 years ago • Ed Siefker

time now, I have read the documentation, but I cannot find any information on what is done with PCR duplicates. My question is then also if recount3 removed PCR duplicates (e.g. with picard or some other tool). Kind regards, Seline

pcrduplicates recount3 multimappingreads

updated 21 months ago • seline.natalie

I am annotating data from a GSE dataset. I want to check that the row.names are equivalent to ID to ensure that there are no mistakes. <code>gse10072 <- getGEO('gse10072', GSEMATRIX=TRUE)<br/> g72...lt;- gse10072[[1]]<br/> total <- pData(featureData(g72))</code> <code>t1 <- data.frame(row.names(total))<br/> t2 <- data.frame(…

geoquery GSE identical row.names

updated 10.4 years ago • PyPer

preformatted">Hi all, Does anyone know if the shortRead package has functionality to filter out duplicate reads, but only reads with more than n duplicates, to avoid reads stacks caused by PCR-aplification? I can only find...srduplicated(), but it doesn't seem to have functionality for specifiying n duplicate reads. Thanks in advance! Regards, JW, Uni. of Copenhagen [[alternative H…

ShortRead ShortRead

updated 15.2 years ago • Johannes Waage

normalisation mat.vsn <- vsnMatrix(RG.final$R) #I try to fit a an object by taking into account duplicate spots (2 spots, spacing=1) fit <- lmFit(mat.vsn, design, ndups=2, correlation=corfit$consensus,weigth=RG$weights[idx...values from this genes and draw the heatmap. The problem is that mat.vsn still contains the duplicate spots, so extracting the values from the normalized matr…

vsn vsn

updated 14.8 years ago • David

class="preformatted">I am looking for references to published papers on microarrays which mention duplicate spots, i.e., replicate spots on the same array containing the same probe. The treatment of the duplicate spots can...be very brief, e.g., just to say that log-ratios from duplicate spots were averaged before further analysis. I am particularly after papers in mainline biological journals

probe probe

updated 21.1 years ago • Gordon Smyth

0200 >From: "Hoen, P.A.C. 't $HKG$" <p.a.c._t_hoen at="" lumc.nl=""> >Subject: [BioC] LIMMA: duplicate correlation >To: <bioconductor at="" stat.math.ethz.ch=""> > >Dear all, >I am analysing results from a spotted microarray...with 9,600 features, >spotted in duplicate. >When I calculate the duplicate correlation, as follows: &…

Microarray Microarray

updated 19.5 years ago • Gordon Smyth

div class="preformatted">Hi Everyone, If I have duplicates in each slide of my experiment, how do I tell limma to handle this? I am using duplicateCorrelation() function, but...all of them, For instance, if there are overall 15000 spots in my experiment, and half of them are duplicates, Shouldn't I end up just with 7500 genes? Thank you for your time. best, -- Andr?s Pinz?n http://bioinf.i…

updated 15.9 years ago • Andres Pinzon

fData(dataSet_final)) <-fData(dataSet_final)$PROBEID</pre> But I get  <pre> Error in `row.names<-.data.frame`(`*tmp*`, value = value) : duplicate 'row.names' are not allowed Besides: Warning message: non-unique value when...setting 'row.names': '227320_at'</pre> My question is,  1. is it normal to have a duplicate probe unremoved after …

expressionset

updated 7.4 years ago • peirinl

them with annotateInteractions() and checked the interactions with isInteractionType() I got duplicate interactions in the data.frame. For example if a connection between 2 annotated regions are in anchor1 and anchor2

duplicate GenomicInteractions

updated 4.8 years ago • dogancan

div class="preformatted">Dear Noah, Only one level of duplication can be handled using the duplicateCorrelation() technique. I suggest that you average over the most highly correlated...duplicate level, which is the side-by-side, then use duplicateCorrelation() for the top and bottom half. E.g., MA2 <- avedups(MA,ndups...From: "Noah Cohen" <ncohen at="" cvm.tamu.edu=""> &…

Microarray limma Microarray limma

updated 18.4 years ago • Gordon Smyth

div class="preformatted">Hi, Some of you may have answers for this. It seems that the duplicate reads are very common in mRNA-seq data. Duplicate reads are those being mapped to exact the same chromosome location

updated 14.1 years ago • jason0701

<div class="preformatted">Hi All I haven't used LIMMA for a while, but I remember that when I did there was a special way to handle duplicate spots. However the layout of the array had to be such that one replicate was printed first for all spots and then the...I haven't used LIMMA for a while, but I remember that when I did there was a special way to handle duplicate spots. However the la…

limma limma

updated 16.7 years ago • Cecilia McGregor

with readGAlignments, I usually set isDuplicate = FALSE  in the scanBamParam argument to remove duplicates. I was just wondering exactly how duplicates are determined--is this based on just chromosome and the start and

genomicalignments rsamtools

updated 8.0 years ago • jfiksel

gt;The duplicated spots have random location, which means that the number of spots between each duplicate is not the same for every gene. This is the summary for the distances: > > Min. 1st Qu. Median Mean 3rd Qu. Max. > 4.00...71.00 86.59 135.00 244.00 > >(Distance here means number of spots between the two duplicates) > >The functio…

limma limma

updated 20.2 years ago • Jason Skelton

vgsID , "GENE.SYMBOL") #then I got Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values when setting 'row.names': ........ ``` I have use the...duplicate() function to check, but the console return FALSE Does anyone have any idea how to solve this? Thanks

DifferentialExpression

updated 2.1 years ago • jscl1n22

the differential binding analysis of some human histone ChIP-seq samples (bowtie2 mapping to hg19, duplicate marking, MACS2 narrow peak calling, blacklisted regions filtering with bedtools intersect and Anshul Kundaje...with the Y vs H comparison: DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length at the point of my script that I was doing a volcano p…

diffbind

updated 5.8 years ago • melnuesch

gene The duplicated spots have random location, which means that the number of spots between each duplicate is not the same for every gene. This is the summary for the distances: Min. 1st Qu. Median Mean 3rd Qu. Max. 4.00 32.00 71.00...86.59 135.00 244.00 (Distance here means number of spots between the two duplicates) The function duplicateCorrelation in limma can be used to…

limma limma

updated 20.2 years ago • Ingunn Berget

<div class="preformatted">Hi, I'm trying to use DESeq to know the differential expressed genes of my datasets and i'm encountering that DESeq is not recognizing my row.names so i can't create my cds. My .csv input file looks like: transcript_id,C4,CRL_2APR10,CRL_1_15JUL11,CRL_2_15JUL11 comp1000201_c0_seq1,5.00,0.00,0.00,0.00 comp1000297_c0_seq1,7.00,0.00,0.00,0.00 comp100036_c0_seq1,0.00…

DESeq DESeq

updated 11.8 years ago • Alicia R. Pérez-Porro

permu.size=10000, Pe=0.001) I got this error <pre> Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values when setting 'row.names': 'cg00042263.ENSG00000146556

HNSC ELMER

updated 6.3 years ago • ghafarpour

an excellent job with limmaGUI! My question is a simple one. The arrays I work with tend to have duplicates on each slide. However, they are not adjacent nor equally spaced and so when setting the spacing of the duplicates...which appears to be compulsory) I just make it up. I presume this makes the correlation between duplicates meaningless but that linear model fits are OK. Comments? Cheer…

limmaGUI limmaGUI

updated 21.4 years ago • Peter Baker CMIS, Indooroopilly

Hi Rory, I had been previously, not marking duplicates or removing them in my ChIP-Seq datasets, and instead setting the dba.count bRemoveDuplicates to TRUE. Firstly

diffbind dba.count bRemoveDuplicates bUseSummarizeOverlaps

updated 6.0 years ago • loretta

<div class="preformatted">Dear List, I had posted earlier about my problem but didn't get any response that could help so I am seeking your help again. I have duplicate spots on my nimblegen array that are position randomized so there is no order to their placement. In Limma when we call the duplicateCorrelation() function, it requires that the duplicate spots have some order to them, lik…

GO limma GO limma

updated 15.9 years ago • Vishal Thapar

Hi,  csaw allows one to remove PCR duplicates when doing read counting across windows. My question is how is this functionality actually executed. I generally...mark duplicates using Picard Tools or Samblaster and I was of the view that csaw would remove these reads when doing read counting...wondering if csaw calls some other program (or its own method) internally for marking and remo…

csaw dedup

updated 8.4 years ago • asif.zubair

software, specifically with the GUI interface and are running into some problems. Our array has duplicate spots in a top to bottom manner. When we try to have Limma calculate a duplicate correlation we get the error message

limma limma

updated 18.7 years ago • Manish Neupane

TRUE) > testFile <- tempfile() > write.table(KarinaSusc, testFile, quote = FALSE, sep = "\t", row.names + =TRUE, col.names = TRUE) > eSet <- read.exprSet(testFile) > eSet Expression Set (exprSet) with 7150 genes 7 samples...sample: arbitrary numbering 2.) Second > KarinaSusc<-read.table("Ka_Susc.txt",header=TRUE,row.names=1,…

updated 21.4 years ago • Marcelo Luiz de Laia

div class="preformatted">Dear List, I was wondering if there is a tool which can help me remove the duplicate probes based on the location of the probes?. To be precise, I wanted to select the probe which is closest to the 3'UTR

probe probe

updated 12.1 years ago • hsharm03@students.poly.edu

than spots that are in the upper and lower half of the array for instance. This means that duplicates that are lets say 10 spots apart probably are more correlated than those 200 spots apart, and I am afraid may "disturb...mistakes during the programming (I''m an R beginner), but I have calculated the correlation between duplicate spots in this way for different methods of background correction …

limma limma

updated 20.2 years ago • Ingunn Berget

I could order the genes and get them next to each other. My question is, how would I incorporate the duplicate correlation aspect when defining the design in limma? Thank you for your reply and help. Yolande [[alternative HTML

Yeast Yeast

updated 16.6 years ago • Yolande Tra

nbsp; We perform our DE analysis with limma+voom packages with clean reads without  PCR duplicates removal. for testing how PCR duplicates would affect DE gene and FPKM value, we also map reads with PCR duplicates...DE analysis with the same pipeline. It turns out that most of the DE genes are overlap in both PCR duplicates removal group and without PCR duplicates removal&…

limma differential gene expression bioconductor

updated 8.8 years ago • panying0713

I realize some areas may map to multiple locations in the genome, but I would like to eliminate duplicates if possible. For example, I have some DMPs that have multiple "hg19_genes_introns" entries. This is a single position...so I would like it to only have one entry. If the number of duplicates were the same for each position, this wouldn't be as much of an issue, because the proportions would …

annotatr AnnotationHub

updated 13 months ago • hayleyw

div class="preformatted">Dear all, On my microarray I have some genes for which I have duplicate probes, but not for all. Before I do the stats I would like to average the duplicate probes (e.g. GB10001-RA and GB10006...ideas what would be the most elegant way to average out expression values based on the occurrence of duplicate entries in RG$genes$GeneName? Limma can only average duplicates i…

Microarray probe limma Microarray probe limma

updated 15.0 years ago • Tom Wenseleers

Hello, I am new here. I have certain numbers of duplicates for each Probe ID (approx. 45000) in one column and its samples data values in others 'n' columns(approx.. 230 columns

aggregateBioVar DEGseq MicroarrayData

updated 3.3 years ago • biomyscience

<div class="preformatted">Hello, There seems to be a problem with read.ilmn() with the new version of limma. When trying to read the control file, there is an error that row names are not unique. x <- read.ilmn(files="probe-profile.txt", ctrlfiles="JAlverdy-JDeF- Dec2-13-ControlProbeData-FinalReport.txt", other.columns="Detection?) Error in `row.names<-.data.frame`(`*tmp*`…

updated 11.1 years ago • Scott Christley

different probenames match the same entrezID which results in an error when I try to assign entrezID row.names : “Error in \`row.names<-.data.frame\`(\`\*tmp\*\`, value = value) : duplicate 'row.names' are not allowed”. topTableOut is output from

clusterprofiler

updated 7.4 years ago • akleens1

Are `AH52264`, `AH66175` and `AH70594` duplicates, arisen due to automated snapshotting of the same resource at different dates? ah <- AnnotationHub() # all ucsc &lt

AnnotationHub

updated 5.4 years ago • Aditya

File"\],source="agilent") However, I get the following error: Error in data.frame(FileName = files, row.names = names, stringsAsFactors = FALSE) :    duplicate row.names: GSM919399\_0361\_ULS\_252483510001\_S01\_GE2\_105...can I tell if E-GEOD-37442 is single-channel or two-color channel 2) How to resolve the issue of duplicate row.names. They appear to have different desc…

differential gene expression limma read.maimages

updated 9.8 years ago • SSK

Total number of duplicates in ChIPQC differs from multiqc ? I check all chromosomes not just one... In fact 0 duplicates are found with ChIPQC...How ChiPQC retrieve duplicate ? How can it be explain ?  Also RelCC is Inf for one of my sample , what does it mean ? &nbsp

ChIPQC ChIPQCreport

updated 7.8 years ago • ZheFrench

getcolproc(CAGE99d) CAGE99p = procset(CAGE99d, colname[3]) and I got following error:- Error in `row.names<-.data.frame`(`*tmp*`, value = c(6995L, 7017L, 7006L, : duplicate 'row.names' are not allowed In addition: Warning message: non...unique values when setting 'row.names': R:A-MEXP-58:210099, R:A-MEXP-58:210100, R:A-MEXP-58:210111, R:A-MEXP-58:210123,R:A-MEXP- [... truncat…

ArrayExpress ArrayExpress

updated 15.5 years ago • Amit Kumar

tdb/potato/microarray_desc.shtml I found that the pattern for replicated spots is non-trivial, duplicates are within a block, but with the upper-left spots duplicated in the lower right of a block, and lower left spots replicated...3) Do something completely different ? Checking the Archive I found very few references to duplicates which are not "columns" , "rows" or "topbottom". Did I miss som…

Normalization Normalization

updated 19.0 years ago • Steffen Neumann

Hi : I have list of `` GRanges `` that needed to apply very specific duplicate removal . I have reason for using specific conditional duplicate removal for my data. However, duplicate removal...condition for each individual `` GRanges `` is different. I want to do complete duplicate removal for first list element; for second list element, I need to search the row that appear more than twice (fre…

r grangeslist duplicate

updated 8.2 years ago • Jurat Shahidin

Hello everyone, I've encountered an issue with the EPIC v2 manifest where I found roughly 12,256 duplicate CpG entries in the column labeled "Name." For instance, cg00002033 appears as a duplicate. However, when examining...literature search, I was unable to find any previous discussions or solutions to this problem. This duplication presents challenges in identifying differentially methylated…

DNAMethylation EPICv2 IlluminaHumanMethylationEPICmanifest

updated 13 months ago • rae.alshammari