Bioconductor Forum

promoters in annotationData that contains just one entry, the function gives an "invalid row.names error". Is this intended? Just for completeness and reproducability, I used the following code: library("ChIPpeakAnno

Annotation AnnotationData Annotation AnnotationData

updated 10.6 years ago • Jens Preussner

tests which was moved and has a new URL. But when I try to push to upstream, I get an error about duplicate commits. I did this: (i) followed the instructions in the page "force Bioconductor master to GitHub master" (ii) cherry...would be informative.  Any advice you can offer would be extremely helpful. thanks, - Sam Duplicate commits: <pre> commit b403a19b826e6f1247c3db382b…

git

updated 6.4 years ago • spollack

div class="preformatted">Hello, I am wondering how to remove duplicate probes from an expression set in Bioconductor. I have tried to use nsFilter with no success. When I use the following

mgu74av2 mgu74av2

updated 12.9 years ago • Angela McDonald

414206 probes and 373 samples.] Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length Can anyone give me a hint what could be the problem? When checking the covariates and the beta matrix I can

champ

updated 6.6 years ago • Gurkenkönig

github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue. > biocLite("mzR") Error in \`row.names<-.data.frame\`(\`\*tmp\*\`, value = aa) :    duplicate 'row.names' are not allowed In addition: Warning message: non-unique...value when setting 'row.names': 'http://rkward.sf.net/R/'  Error in \`row.names<-.data.frame\`(\`\*tmp\*\`, v…

mzR

updated 10.1 years ago • amrahweijn

<div class="preformatted">Dear Bioconductor list: Could anyone provide a good explanation on "duplicateCorrelaton"? There are two one-channel non-Affymetrix data sets in each of which each gene was spotted twice on each chip. To estimate correlation between duplicate values, I ran regular cor.test for each gene across all chips. The results showed average cor values as 0.52 and 0.81...data…

updated 19.1 years ago • Jianping Jin

div class="preformatted">Hi When ignoring duplicate spots, the functions "readTargets", "modelMatrix" and "makeContrasts" helps to construct the design matrix. Are there...similar functions for "automatic" generation of the design vector when considering duplicate spots using "duplicateCorrelation" and "gls.series"? Looking forward hearing from you! Jakob -----------------------------------…

updated 20.7 years ago • Jakob Hedegaard

<div class="preformatted">Dear Mitch, You don't say what instructions you are trying to follow here. I think you may be trying to use code which was intended for other data sets. I suspect that there may be more than one problem. Firstly, why do you need to use readGAL()? This is only needed with SPOT data. Your RG object from read.maimages() will already contain annotation information fr…

limma limma

updated 17.9 years ago • Gordon Smyth

arrays. I have 3 Bioreps each having 1 technical rep. There are no dye swaps. In each rep, there are duplicate spots on the array. In this experiment, as I reconstructed the images from the data, I see some "quite" bad spots in the...do you handle the statistical confidence with your results if you do or dont? 2) I want to use the duplicate spots on each rep for my analysis. As of now, I do the …

Normalization limma Normalization limma

updated 15.9 years ago • Vishal Thapar

Hi. I have used DESeq2 to performed differential analysis.  And now I would like to plot the data using transformed values "rld", but not sure how to determine the means for the biological duplicates. The simplest way I could think of is use the arithmetic means. For normal log transformation, that would means using...the data using transformed values "rld", but not sure how to determin…

deseq2

updated 7.9 years ago • JunLVI

concatenating the reads from other samples, and so I wondered if the reads are being filtered out as duplicates. If so then is there a way to override this option? Please see the code below for your reference. Appreciate all the...allowed.mismatch.PAM = 2, overwrite = TRUE) Remove duplicate reads

GUIDEseq

updated 2.7 years ago • sharvari gujja

For example 3 genesets have genename caspase 3; 3 genesets are called caspase 9 and there are duplicates for caspases 8, 14, 7 and more. The next problem is that there is in most cases very little correlation between the

mouse4302 mouse4302

updated 16.1 years ago • Paul Geeleher

Hello again,   after installing succesfully the packages and reproducing all examples, I would like to analyze my own mutation calls. I have a problem importing my vcf file - sorry if these are naive questions but I am really new here.   <pre> <span style="background-color:rgb(225, 226, 229)">> fl=readVcf("Ac216_H69_1_A549_mutect_confident_eff.vcf", "hg1…

variantannotation somaticsignatures

updated 10.4 years ago • Anna N.

going well, except in aCGH (Jane Fridlyand) I'm unable to get the acgh.process command to run with duplicate removal = TRUE. It works if dupRemoval is set to False This is what I get: #> ex.acgh<-aCGH.process(ex.acgh, chrom.remove.threshold...unused argument(s) (drop = FALSE) #> Would be grateful if anyone has any tips on how to handle duplicate clones in aCGH. Thanks ver…

aCGH aCGH snapCGH aCGH aCGH snapCGH

updated 17.7 years ago • Ian Roberts

though I am looking for differential abundance of microbial genera, not gene expression. However, duplicate genera (assigned to different species in my taxa table) are listed out and numbered instead of collapsing. I would...like to collapse duplicate genera. ![enter image description here][1] Here is what I ran to generate my figure: ```deg_plus1 <- transform_sample_counts

DESeq2

updated 21 months ago • Bretta

a section on Within-Array Replicate Spots. But only mentions what to do for people who have a single duplicate of every spot on their array. I'm sure other people have had to deal with this in the past. Do you have any pointers? Thanks

limma limma

updated 17.2 years ago • Yannick Wurm

Error in processAmplicons("Index2.Plate10.fastq", barcodefile = "Samples1.txt",  : There are duplicate hairpin sequences. I am kind of at a loss here. I don't know what to fix. Thanks, Lucia

processamplicons

updated 8.9 years ago • lucia.caceres

both block and ndups: > >"At this time it is not possible to estimate correlations between >duplicate spots and between technical replicates simultaneously. If >block is not null, then the function will set ndups...I have 3 Bioreps each having 1 >technical rep. There are no dye swaps. In each rep, there are duplicate >spots on the array. In this experimen…

Normalization limma Normalization limma

updated 15.9 years ago • Jenny Drnevich

and resulted in some changes in the lists of DE genes. All of this suggests to me that loess and duplicate correlation served to reduce the estimate of variance in gene expression and weed out artifacts. However because

Normalization Normalization

updated 20.0 years ago • Dennis Hazelett

div class="preformatted">Is there any general procedure for handling duplicate genes in Affy arrays? For example, for the hu6800 array which has 7129 probe sets, there are 869 genes that are represented

hu6800 probe hu6800 probe

updated 19.6 years ago • jsv@stat.ohio-state.edu

bytes (4.0 MB) ================================================== downloaded 4.0 MB Error: Duplicate identifiers for rows (75, 83), (76, 84), (77, 85), (78, 86), (79, 87), (80, 88), (81, 89), (82, 90) Please suggest me the solution.     &nbsp

geoquery getgeo

updated 7.0 years ago • umahajan

In the PureCN coverage QC file, are the mean duplication columns in FRACTIONS OF READS that are duplicated, or in X (number of reads that are duplicated)? Also, several of

PureCN coverage

updated 6.9 years ago • twtoal

So am using the following code #just.raw.counts = read.delim("Raw_counts_input.txt", row.names=1) #meta.data = read.delim(file="meta_data.txt", row.names = 1) #count.data.set <- DESeqDataSetFromMatrix(countData...code I get an error #Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed Below…

microbiomeExplorer tartare projectR

updated 4.1 years ago • amoaristotle

gt; (http://www.bioconductor.org/packages/devel/bioc/html/vsn.html) does not > output the row.names (the corresponding probe sets names). Can this be > something related to changes in the AffyBatch object? > > Roumyana

probe vsn probe vsn

updated 17.0 years ago • Wolfgang Huber

end 150bp RNA-seq data with approx 35M paired reads per sample. dupRadar is showing relatively low duplication rate for genes with high expression level (see the scatter plot - [https://freeimage.host/i/dhW3Cu][1]). Could it be an

dupRadar 150bp RNA-seq

updated 4.6 years ago • olegderyagin

<div class="preformatted"> Hi Adrien "biologically": has to do with the work flow from collecting the eukaryotic sample to the point where you have intensity data, in these kind of experiments. "pitfall" (one of them): try taking a look few probesets of this nature (multiple for each transcript) in some experiments and your favorite expression summary measure and see what you get. …

hu6800 probe affy hu6800 probe affy

updated 19.6 years ago • Suresh Gopalan

Hello, I need to remove duplicates in the `animal_id` column. I tried using `tidySummarizedExperiment` make the code more reproducible. However, `distinct...counts = assay_data), colData = sample_data ) print(colData(tse)) # Need to remove animal_id duplicates #> DataFrame with 10 rows and 3 columns #> animal_id treated disease #> <factor> <f…

dplyr TreeSummarizedExperiment

updated 17 months ago • question_guy

either, or I don't understand the process correctly): when I am exporting the csv file, there are duplicate entries for some gene names (i.e. ESR1). I am under the impression that RMA and the process I am using (target = 'core') summarizes...at the gene level, so I am not sure why I am getting duplicate entries for certain (not all) genes after writing the expression file. I have gone through t…

Annotation PROcess Annotation PROcess

updated 10.9 years ago • Guest User

We attempted the following: > library(limma) > targets <- readTargets("targets_file", row.names = "Name") > RG <- read.maimages(...) > RG.c <- backgroundCorrect(...) At this point we have an RG and RG.c objects that contains...However, that simply duplicated Red and Green values. For 3 chips we had a set of 3 red and 3 green duplicates. So, onc…

GO limma convert GO limma convert

updated 16.1 years ago • Boris Umylny

Please Help!   Why does getGEO return "Error: Duplicate identifiers for rows"? How can this error be fixed?  This getGEO command was working fine for a week and then Stop...locally cached version: D:\\I\_\\\_Gene\\R\\desktopBrstC/GSE76275\_series\_matrix.txt.gz Error: Duplicate identifiers for rows (4506, 4771), (4508, 4773), (4510, 4775), (4511, 4776), (4512, 4777…

getGEO

updated 7.3 years ago • cg

I have repeated sampling of the same individuals I consider it would be appropriate to use Limma and Duplicate correlation (in comparisons involving paired samples) - correct? Q2) We have discussed using Deseq2 as well, but if...I understand, the duplicate correlation function is not available there and therefore it is better to use the code above and limma in the entire...and how and where ca…

RNASeqR

updated 3.9 years ago • sofie.haglund

Hello, I am trying to annotate an SCEset using getBMFeatureAnnos where the filter column contains values such as "MTCE.31" and "MTCE.23". In making the SCEset these are recognized as different row names, however when running the getBM function the ".31" and ".23" are ignored and they are interpreted as duplicate row.names. Is there another way to format the column to get around this? Thank you …

sce biomart annotation

updated 7.7 years ago • linda.c.dansereau

<div class="preformatted">Dear Christine, duplicate correlation in limma is only for replicate spots which are regularly spaced. The spacing value is the number of spots between replicates. Your value of 21 cannot be correct on an array with 16 columns and 11 rows, and that is what limmaGUI is telling you. You haven't actually told us how the 4 replicates for each mir are arranged on th…

GUI limma limmaGUI microRNA GUI limma limmaGUI microRNA

updated 16.4 years ago • Gordon Smyth

so I'm not sure when the change happened). In R 3.1.3,  select() would give you a warning about duplicate query keys, but would still give you all the mappings: <pre> R version 3.1.3 (2015-03-09) -- "Smooth Sidewalk" #lines removed...in 1:many mapping between keys and return rows > dim(all.sgd.go) [1] 87827 4 > > #duplicate just a few SGD: &gt…

AnnotationDbi

updated 9.3 years ago • Jenny Drnevich

have two samples, one is case, one is control. ecs <- estimatelog2FoldChanges( ecs ) Error in `row.names<-.data.frame`(`*tmp*`, value = c("geneID", "exonID", : duplicate 'row.names' are not allowed In addition: There were 50 or more warnings

DEXSeq DEXSeq

updated 11.1 years ago • Fabrice Tourre

that has some negative values once the background has been subtracted from the spots. These are in duplicate so I am using the dupcor.series method. This works ok until I try and add in the backgroundCorrect method=minimum

limma limma

updated 21.0 years ago • Helen Cattan

end") cds <- DESeqDataSetFromMatrix(cnt, colData, design=~group) here I have faced an error: Duplicate rownames not allowed. I found that the problem is not with the rownames, itis the culnames. so, I choose a unique name

deseq2

updated 6.0 years ago • Yasavoli.h

right hand side). I use limma to do my analysis. I know at the moment it is not possible to treat duplicate spots, technical replicates and biological replicates, but I though if I use the duplicateCorrelation function...on my duplicate spots, and then to use a contrast matrix to average of all of the Treated vs Non-treated biological samples, I could...MU10vsWT10)/10, levels=design)> &…

limma limma

updated 15.0 years ago • Ana Staninska

to use open TG-gates and drugmatrix data to do toxicogenomics analysis. Within the data, there is duplicate or triplicate data for each different dose of different chemicals. I arranged the data as this Chem_Name Class

microarray limma

updated 4.7 years ago • peirinl

Hope that helped :) Best, Naira -------- Original Message -------- Subject: Re: [BioC] Duplicate probesets in mouse4302 Date: Tue, 3 Feb 2009 17:36:03 +0000 From: Paul Geeleher <paulgeeleher@gmail.com> To: Naira Naouar...example 3 genesets have genename caspase 3; 3 >> genesets are called caspase 9 and there are duplicates for caspases 8, >> 14, …

mouse4302 cdf mouse4302 cdf

updated 16.1 years ago • Naira Naouar

recommended to use the DESeq function to perform differential analysis for it treats the samples as duplicates when calculating dispersion. Does the rlog function do the same thing? Should I use simple log transformation

deseq2

updated 8.9 years ago • Chao-Jen Wong

PQ2A" "PQ2B" "PQ3A" "PQ3B" > d<-raw.data[,2:13] > rownames(d)<-raw.data[,1] Error in `row.names<-.data.frame`(`*tmp*`, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique value...when setting 'row.names': ?????? -- Sent via the guest posting facility at bioconductor.org. </div

edgeR edgeR

updated 11.0 years ago • Guest User

<div class="preformatted">in RNA-seq data analysis, do we need remove PCR duplicate before we look for DE (differential expressed)genes some people say yes, some say no -- shan gao Room 231(Dr.Fei lab) Boyce...div class="preformatted">in RNA-seq data analysis, do we need remove PCR duplicate before we look for DE (differential expressed)genes some people say yes, some say no -- shan ga…

updated 11.8 years ago • wang peter

topTable(fit.contrast, adjust.method="none", coef=c(1:4), number=20000, p.value = 0.05) Error in `row.names<-.data.frame`(`*tmp*`, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values...when setting 'row.names': I have tried to run the same script for each coefficient separately and it works fine. I can't explain the error since...if the…

updated 11.4 years ago • Christian De Santis

<div class="preformatted">Gordon Smyth <smyth ...="" at=""> writes: > > I really hesitate to explain how to average of duplicate spots using limma, > because it is not something I generally recommend. It is however quite easy: > > Start with a normalized MAList object, 'MA', possibly containing spot > quality weights. Suppose that there are '…

updated 16.9 years ago • Sanjat Kanjilal

168,7 +168,7 @@ }, dups) if (length(dups)) .warningf("%d record(s) contain duplicate ids: %s", - length(dups), selectSome(sort(ls(dups)))) + length(dups), paste(collapse=", ",selectSome(sort(ls(dups))))) GeneSetCollection

gseabase bug

updated 8.5 years ago • dondelelcaro

I keep getting different errors all of a sudden and I don't know why I've been getting either: duplicate 'row.names' are not allowed when I delete row.names I get: ncol doesn't equal ncount or I get that there are neg values...gt; > gene_count_matrix <- > as.matrix(read.csv("/home/gordovezfa/R/3.5/Shawn/file.csv", row.names > = "gene_id")) View(gene_count…

deseq2

updated 5.7 years ago • skamboj

div class="preformatted">Hi, My cDNA array have 2 duplicate for each spot. I read and normalize my data set in limma. I use the result MAList (MA) object in timecourse package. But

TimeCourse limma timecourse TimeCourse limma timecourse

updated 18.2 years ago • Marcelo Laia

in VariantAnnotation I get an error message   Error in DataFrame(Samples = seq\_along(colnms), row.names = colnms) : duplicate row names     What may be causing this? I am not sure how I ended up with duplicate names in

variantannotation readvcf

updated 10.4 years ago • JK

nbsp;   Starting  100 permutations...  Computing pfp...  Error in \`row.names<-.data.frame\`(\`\*tmp\*\`, value = value) :    invalid 'row.names' length" I have been stuck with this for a really long time

rankprod microarray

updated 9.7 years ago • sumedharoy

Hi,  I have used Salmon to quantify some 126 samples using the mouse ensembl reference cDNA transcriptome. Then I tried to obtained  abundance values using tximport as follows: <pre> txi.salmon <- tximport(files, type = "salmon", tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM", ignoreTxVersion = F) names(txi.salmon) head(txi.salmon$counts) ###C…

tximport deseq2

updated 6.6 years ago • ctl

div class="preformatted">I really hesitate to explain how to average of duplicate spots using limma, because it is not something I generally recommend. It is however quite easy: Start with a normalized...MAList object, 'MA', possibly containing spot quality weights. Suppose that there are 'ndups' duplicates at spacing 'spacing'. You can average over duplicates by fit1 <- lmFit(MA, des…

limma limma

updated 19.9 years ago • Gordon Smyth

1022045 [1] 1025088 [1] 1025088 Shouldn?t the lengths of these all be identical? Also, I am seeing duplicate values for the x_y coordinates. For example, it is saying there are 8 probes with x_y coordinates of 1000_198, and

probe affy PROcess oligo probe affy PROcess oligo

updated 10.8 years ago • Stephen Piccolo

in page 6, I get the following error ```Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed Además: Warning message: non-unique values when setting 'row.names': ‘TCGA-50-5066’, ‘TCGA-50...5946"``` I confirm that I get TRUE twice, in rows just one after another. So there seems to be a duplicate subject here that was maybe added to the data after th…

MultiAssayExperiment cBioPortalData

updated 3.9 years ago • Javier

downloaded 108.0 MB Unpacking data files ArrayExpress: Reading pheno data from SDRF Error in `row.names<-.data.frame`(`*tmp*`, value = c("US10020348_252800421889_S03_GE2_107_Sep09_1_1.txt", : duplicate 'row.names' are not...allowed In addition: Warning message: non-unique values when setting 'row.names': ‘US10020348_252800419789_S01_GE2_107_Sep09_1_1.txt’, ‘US10020348_2528004201…

arrayexpress twochannel microarray

updated 7.4 years ago • Andy91

this analysis, I am using the Limma package. The experiment design involves 3 kinds of replicates: duplicate spots (within array replicate), technical replicates (as dye swap), and biological replicates. I know that at the moment...it is not possible with limma to treat this kind of experiment, but I have an idea how to avoid duplicate spots (within array replicates), if that is possible. So here…

Microarray limma Microarray limma

updated 15.1 years ago • Staninska, Ana, Dr.

<div class="preformatted">Dear List, I have a set of mouse affy data. They platform is Affy mouse 430a2 chip. There are 8 samples , 4 for each condition. I normalized the data using rma. The array has 22090 probes originally. Then, in order to filter out the genes which have no entrez id, are duplicates for the same gene, I used the following command . filter <- nsFilter(eset1,requi…

Annotation mouse4302 annotate affy Annotation mouse4302 annotate affy

updated 12.2 years ago • hsharm03@students.poly.edu

error density.default(newX[, i], ...) : 'x' contains missing values Warning message: duplicate row.names 12,15,20,21,22,25,26,27,31,32,33,34,38,39,40,43,44,45,48,49,50,54,55,5 9,60,64,65,69,70,73,74,75,78,79,83,84,88,89,90,94,95,96...480,483,486,490,491,493,495,498,501,504,506,507,509,510,512,513,5 [... truncated] in: data.row.names(row.names, rowsi, i) How can I do for next step to de…

cdf affy affyQCReport cdf affy affyQCReport

updated 16.6 years ago • Yisong Zhen

the last line above): """ Error in read.table(file = file, header = TRUE, col.names = allcnames, : duplicate 'row.names' are not allowed """ I'm not sure what its referring to as both files have duplicate gene names (which I presume

updated 16.0 years ago • Paul Geeleher

this error. Error in read.table(URL, sep = "\t", quote = "\"", fill = TRUE, comment.char = "", : duplicate 'row.names' are not allowed My generic code is something like this. kegga(list(Up=up, Down=down), species="Hs", universe

limma goana kegga

updated 5.5 years ago • Ahdee