Bioconductor Forum

VCF requires unique row names, but the formula used to generate placeholder row names can produce duplicates (Such as for pindel with default parameters run on the NA12878 Illumina platinum genomic WGS data). Is this intentional...VCF requires unique row names, but the formula used to generate placeholder row names can produce duplicates (Such as for pindel with default parameters run on the NA12…

variantannotation

updated 8.9 years ago • Daniel Cameron

at="" gmail.com=""> > Subject: [BioC] how to use normalizeForPrintorder accounting for > duplicates when there are spots that are not duplicated in the array? > To: "Bioconductor List" <bioconductor at="" stat.math.ethz.ch

Microarray limma Microarray limma

updated 17.7 years ago • Gordon Smyth

the package and it returns this error: Error in data.frame(binary= binvers, source = srcvers, row.names = bins,  : duplicate row.names: R.utils So I try to load the package with ... library(oneChannelGUI) and this returns

microarray software error bioconductor

updated 9.4 years ago • o.j.james

<div class="preformatted">Paul Geeleher <paulgeeleher at="" gmail.com=""> writes: > Hey Everyone, > > I'm having a problem reading some single channel GenePix data. > > I use the following code to read the files: > > # define column names > Cy3 <- "F543 Median" > Cy3b <- "B543 Mean" I don't think these are …

Cancer Cancer

updated 16.0 years ago • Martin Morgan

on the right side So...The experiment design involves 3 kinds of replicates: within array replicate (duplicate spots), technical replicates (as dye swap), and biological replicates. I know that at the moment it is not possible...limma to treat this kind of experiment, but I have an idea how to avoid duplicate spots (within array replicates), if that is possible. Here I need your help. There are…

Microarray limma Microarray limma

updated 15.1 years ago • Staninska, Ana, Dr.

I am new to RNAseq and started to analyze my dataset using DESeq2. I first run the `DESeqDataSetFromMatrix` function and found the error message ``` Error in DESeqDataSetFromMatrix(countData = HitCount, colData = myCondition, : ncol(countData) == nrow(colData) is not TRUE ``` In addition, if I run the following code I get this warning: ``` all(colnames(HitCount) == myCondition$SampleID) [1]…

DESeq2

updated 11 months ago • ussarizona

the p-values listed in toptable were all different, the adjusted p-values (adjust="BH") contained duplicate values. I don't think this is incorrect necessarily, but I was wondering why a different alpha wasn't generated for

updated 13.5 years ago • David Young

see which cell line expresses higher level of what genes. The problem is, I did not do any duplicates, so I only have one sample per each cell line, and when I tried doing `dds1 <- DESeq(dds1)` it tells me: The design matrix

DESeq2 FeatureCount

updated 2.5 years ago • Jiayi

timepoints sequenced by 10x and would like to compare them against each other. They are all in duplicates (two biological replicates for each TP). How would one go ahead with duplicated? Do I need to merge the two biological

scRNA zinbwave batch IntegratedData

updated 4.5 years ago • Assa Yeroslaviz

<div class="preformatted">Hello ! I am comparing the transcriptome of two yeast strains, A and B. For each strain we have 5 biological replicates. The strains are compared to a reference on two-color arrays. For each biological replicate, we used two slides, in dye-swap. So we have 20 slides : slide Cy3 Cy5 1 A1 ref 2 ref A1 3 A2 ref 4 ref …

Yeast limma a4 Yeast limma a4

updated 16.4 years ago • sylvie pinloche

genes<-readGAL('fish.gal') > RG$printer<-getLayout(RG$genes) > maQualityPlots(RG) Error: duplicate switch defaults: 'list(dev =...' and '' > sessionInfo() R version 2.13.0 (2011-04-13) Platform: i386-pc-mingw32/i386 (32-bit) locale

arrayQuality arrayQuality

updated 13.8 years ago • Fabio Liberante

Hi everyone: I have set of compressedList in the multiple list where each compressedList are corresponds to overlap position index of one set of genomic interval to another, and the order of compressedList in each list are very different. However, I am trying to integrate these multiple compressedList into one without duplication. To make things clarify, this data are the result of finding ov…

r iranges findoverlaps IntegerList List

updated 8.3 years ago • jian_liangli

next to each other. Do you know a solution? Also another question: IF one day I manage to do the duplicate correlation and given that I would use weights to identfy features with the flag "bad", how will the software handle

GUI limma microRNA GUI limma microRNA

updated 16.4 years ago • Christine Voellenkle

Running PureCN.R v 1.13.21, I get this warning and these "null device" messages. Are they something to be concerned about? ``` ...snip... INFO [2019-04-29 15:42:06] Fitting variants for purity 0.37, tumor ploidy 3.73 and contamination 0.01. Warning message: In .bcfHeaderAsSimpleList(header) : duplicate keys in header will be forced to unique rownames INFO [2019-04-29 15:42:06] Fitting…

PureCN

updated 5.9 years ago • twtoal

Hi, When converting a GInteractions object into a dataframe, a ‘duplicate row.names’ error is generated. This is presumably a problem with the as.data.frame function, which encounters...gt; as.data.frame(GInt) Error in data.frame(seqnames = as.factor(seqnames(x)), start = start(x), : duplicate row.names: name_1, name_2, name_3, name_4 > GInt <- GInteractions(unname(Gran…

InteractionSet

updated 3.7 years ago • noa

me " There are samples duplicated. We will not be able to prepare it" How do I get rid of the duplicate files? My code and session ``` > library(TCGAbiolinks) > library(xlsx) > library(DT) > library(edgeR) > library(org.Hs.eg.db

TCGAbiolinks

updated 3.4 years ago • raf4

on core_mps... OK Saving DataFrame object for PM. Saving NetAffx Annotation... 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': ‘’  </pre

annotation microarray pdinfobuilder oligo

updated 8.5 years ago • Ed D

and geo\_accession fields moreover that I faced also critical obstacle with duplicated “row.names” , could any one directive me how I can overcome to that essentially dogma, please. Thank so much for any one will suggest

recount summarizedexperiment

updated 7.3 years ago • Mustafa ABUELQUMSAN

fit2$t[,2], index=indices[["GO:0001780"]] ) Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values when setting 'row.names': ‘100506380’, ‘143872...84631’, ‘8553’ </pre> How can i fix this issue ? i should remove prior the mroast function these duplicates ? Thank you in advance, Efstathios

limma mroast agilent microarrays GO.BP barcodeplot

updated 6.4 years ago • svlachavas

limma user's guide 9.6   targets <- readTargets("AllTimePointFiles.csv",path=datadir,sep=",",row.names="filename") data <- ReadAffy(celfile.path=datadir) eset <- affy::rma(data)   X <- ns(targets$TimeType,df=2)   \# the

limma microarray affy

updated 7.9 years ago • tjest

one for asking it. I am studying the gene expression of a species that has undergone a duplication event. I have a synteny table of gene duplicates for multiple tissue types, which was derived using the genome...of a related ancestral species (that existed prior to the duplication event). I want to identify loci where the duplicates have significantly different expressions - I was wonderin…

rnaseq DESeq2

updated 15 months ago • pl23

expressed genes between a wild-type (Ctl) and mutant (Mut). The mutant has a large DNA duplication encompassing several hundred genes, so they always come up as ~2x upregulated but this is not biologically interesting...tt_2 <- run_cf_eb(H0 = 2, fit) ## H0 is 'ctl = 2 x mut' ## tt_all <- merge(tt_1, tt_2, by = 'row.names', suffixes = c('.H0_1','.H0_2')) ## Plot logFC from H0('ct…

differential gene expression limma rnaseq design and contrast matrix limma voom

updated 9.1 years ago • stuart

one from package ‘S4Vectors’: not turning on duplicate class definitions for this class. Note: the specification for class “SimpleList” in package ‘IRanges’ seems equivalent...to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class. Note: the specification for class “characterORNULL” in package ‘IRanges’ seems...to one from package ‘S4Vectors’: not turning…

org.hs.eg.db

updated 9.6 years ago • alok.jaiswal

1\] rownames(countdata1)<-countdata1\[, 1\] I get the following error:  duplicate 'row.names' are not allowed I have tried so many ways of trying to get this to work, trying solutions other people have

deseq2 countdata

updated 7.1 years ago • A

I keep getting from DESeqDataSetFromMatrix function is "Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed." I appreciate any advice you can provide. Code should be placed in three backticks as shown...design=~sex, tidy = TRUE) # The error I get is: Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed In addit…

DESeq2 Bioconductor

updated 3.0 years ago • Kevin

carrying out separate channel analysis of two-color data in limma. I find that I can not merge the duplicate spots on the arrays. The function lmscFit() does not provide an argument "ndups" to deal with the duplicate spots on...the arrays as lmFit() does. Therefore there are many duplicate spots in the DE genes. I wonder whether there is a way to merge the duplicate spots. Thanks Dejian <…

updated 16.2 years ago • De-Jian ZHAO

Hello, I have been trying to use makeTranscriptDbFromGFF() to read my gff file but I get the following error: extracting transcript information Error in .prepareGFF3TXS(data, useGenesAsTranscripts) :   Unexpected transcript duplicates In addition: Warning message: In .local(con, format, text, ...) :   gff-version directive indicates version is &nbsp…

genomicfeatures

updated 10.1 years ago • Miss Agnieszka Aleksandra Golicz

Dear List, I am trying to duplicate the analysis using csaw in the paper, "From reads to regions", https://pubmed.ncbi.nlm.nih.gov/26834993/ I received...out <- suppressWarnings(sortBam(bam, "h3k9ac_temp")) file.rename(out, bam) } # Mark duplicates temp.bam <- "h3k9ac_temp.bam" temp.file <- "h3k9ac_metric.txt" temp.dir <- "h3k9ac_working" dir.create(temp.dir

chipseq csaw; crosscorrelation

updated 3.8 years ago • richardallenfriedmanbrooklyn

I conducted differential expression analysis using limma over several datasets separatly. Now I have several dataframes containing the differential expression analysis for those datasets, and I want to show them on a volcano plot using the MetaVolcanoR package. If it matters, each dataframe contains a different number of genes. All of them together have about 1900 genes, with 322 duplicate genes…

limma MetaVolcanoR EnhancedVolcano

updated 2.7 years ago • JAcky

other. >Do you know a solution? > >Also another question: >IF one day I manage to do the duplicate correlation and given that I would >use weights to identfy features with the flag "bad", how will the software &gt

GUI limma microRNA GUI limma microRNA

updated 16.4 years ago • Naomi Altman

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

<div class="preformatted">Dear Paul, While I know what this error is, I haven't seen it arise previously in duplicateCorrelation() with microarray data, so it is hard to give advice. It is a numeric error in the inner optimization routine which may arise for reasons which are hard to pin down. Try removing rows from the hx object, e.g., run duplicateCorrelation() on the top half or bottom…

Microarray probe Microarray probe

updated 15.5 years ago • Gordon Smyth

am working on a data that use fibroblast RNA-seq result. Another samples have multiple experimental duplicates for each data point which is nice. Some have 3 or more and some have 2 duplicates. I believe it is still ok to use 2 duplicates...DESeq2. My problem is that for the original sample, fibroblast, they only provide 1 sample without duplicates. I understand that fibroblast is quite general c…

rna-seq deseq2

updated 6.0 years ago • bharata1803

div class="preformatted">I have a data set which pretty much duplicates the experimental design of one of the limma examples, so I am using that with great results :-D There is one difference...though - the limma example has no duplicate spots, whereas my design does. So I did two runs of limma, one to find differentially expressed spots, the other to...differentially expressed genes (I assu…

limma limma

updated 20.7 years ago • michael watson IAH-C

control probes using package illuminaHumanv4.db Version:1.26.0 Error in value[[3L]](cond) : duplicate row.names: 200647550006 AnnotatedDataFrame 'initialize' could not update varMetadata: perhaps pData and varMetadata

beadarray iscan

updated 7.9 years ago • S. K.

rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : A specification for S3 class ???terminal...rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, …

BiocInstaller cummeRbund Gviz BiocInstaller cummeRbund Gviz

updated 12.0 years ago • Guest User

fish.gal') > > RG$printer<-getLayout(RG$genes) > > maQualityPlots(RG) > Error: duplicate switch defaults: 'list(dev =...' and '' > > sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: i386-pc-mingw32/i386 (32

arrayQuality arrayQuality

updated 13.5 years ago • Ignacio Lopez De Ullibarri Galparsoro

I wonder that whether the input bam file need to be the raw bam files which include the chrM, duplicates. When I tried to input the bam file (q30) which was removed the adapters,duplicates, chrM, the fragment distribution...lt; 100bp (which was considered as nucleosome free region) was similar with around 200bp. The duplication rate is 34%, the %chrM of filtered bam is 50%. Thank you in …

ATAC-seq ATACseqQC

updated 5.7 years ago • Shuang He

In the csaw workflow and vignette, it is mentioned that duplicate removal is not always advisable. I couldn't quite understand why that would be. Shouldn't duplicate removal help

csaw dedup

updated 8.9 years ago • asif.zubair

SNP), dendrogram construction and estimating the error rate between replicated samples (duplicates/triplicates). My code : mat <- 1-ibsmat mat1 <- mat[-99:-100,-99:-100] #ERROR RATE FOR triplicates x <- seq(1,274,3) err.r <- rep...ibx[lower.tri(ibx)]) } errorrate <- mean(na.omit(err.r)) #ERROR RATE FOR…

R SNP genotyping genetic diversity

updated 6.2 years ago • meriam.nef

all samples) and I have the following samples to work with: 0h - No treatment, a single set of duplicate samples collected 2 days - duplicates collected for drug treatment and DMSO control 10 days - duplicates collected...for drug treatment and DMSO control 42 days - duplicates collected for drug treatment and DMSO control My goal with the analysis is two-fold. First, I want to identify …

RNASeq DESeq2 timecourse

updated 14 months ago • WS

and I would like to have suggestions on the methods I should use to analyse the data. I have three duplicates done in two different places, so they look very different in terms of background and signal intensities. Since...I'm not going to have more duplicates I would like to get the most information possible from these, even if I do know that it is not the perfect experimental...I just compare …

Microarray Microarray

updated 21.0 years ago • Paola Sgado'

48hr ----------------------------------------------- My previous approach in my analysis was to duplicate the 0hr data point to create a control and treatment variation: ------------------------------------------------- Control 0hr,4hr,8hr,12hr,16hr,20hr,24hr,48hr vs Treatment...I am very much a beginner: >counttable <- read.csv("~/Desktop/Countsdata.csv", header=T, row.names=1)…

updated 12.2 years ago • Marcelo

Hi, I was trying to analyze a dataset with a slightly high number of duplicates, (i.e. the duplication rate at the lower end of the expression (reads/kbp) seems to be high at ~ 25%). I am therefore not too

deseq2

updated 5.1 years ago • Brian Smith

div class="preformatted">Hi-- apologies if this is a duplicate email. I just joined the list today and I didn't know how long the email I just sent before I joined would be under moderator...just keep GSM } } if(!exists("affyobj")){ mdExprs <- as.matrix(read.csv(defaultExprs,row.names=1)) if( min( mdExprs, na.rm = TRUE ) >= 0 & max( mdExprs, na.rm = TRUE ) &gt…

GO Cancer GO Cancer

updated 13.4 years ago • Ben Ganzfried

object: library(graph) g <- graphBAM(data.frame(from="1", to="2", weight=1)) edgeMatrix(g, duplicates=FALSE) [,1] from 1 to 2 edgeMatrix(g, duplicates=TRUE) ## here is the problem !! [,1] from 1 to 2 edgeMatrix(as(g, "graphNEL"), duplicates

updated 11.7 years ago • Robert Castelo

div class="preformatted">Hello folks, I'm getting this error when I run duplicate correlation: corfit <- duplicateCorrelation(mat@hx, design, ndups=3, spacing=1) Error in glmgam.fit(dx, dy, start = start

updated 15.5 years ago • Paul Geeleher

data set. I can calculate the standard deviation using simple function sd( ). But there the spot duplicates are not taken into account, only slide replicates. After running lmFit(), eBayes() and topTable() the duplicates are

updated 20.1 years ago • Sebastian Thieme

for expressions. I used the following commands: data<-ReadAffy(widget=TRUE) (Read in 2 sets of duplicate arrays, 4 total) eset<-rma(data) se.exprs(eset) A matrix (of the appropriate dim) is returned, but all the entries are...the expresso command (for MAS preprocessing) and got the same results. Any suggestions? BTW, are duplicate arrays required in order to get standard errors?…

updated 21.9 years ago • Ann Hess

Hello all, I am sorry for this, but I need to retract my request for help. I am not sure LimmaGUI can cope with replicates in the same block (as this gal file shows). I was not expecting them to be in the same block and am getting the files checked. Sorry to have wasted anyone's time, but I might be back once this problem is sorted out... Thank you and my apologies again, Liz Brooke-Powell …

limmaGUI limmaGUI

updated 19.8 years ago • Brooke-Powell, Elizabeth

<div class="preformatted"> Hi, Can anyone help me with the following please? I have an experiment using two sets of arrays with different layouts and therefore different GAL files that I need to analyse together. A previous suggestion on this mailing list was to normalize and then combine the log ratios. Can anyone tell me what the code for combining 2 MALists is please? Secondly one of …

updated 20.9 years ago • Helen Cattan

<div class="preformatted">Hi, In lmFit(object, correlation), "correlation" is "the inter-duplicate _or_ inter-technical replicate correlation". Correlation is calculated using duplicateCorrelation(object, ndups, block), where "ndups" is the number of spot replicates, and "block" is used to describe technical replicates. The help entry for duplicateCorrelation() says that "At this time it…

updated 16.6 years ago • Dries Knapen

ids. Some are ncRNAs on different locations of the chromosome. I am wondering how you deal with duplicates prior to CPM filtering, TMM normalization, and designing the matrix - do you sum or average the read counts per duplicated...gene across all samples or do you remove all instances of duplicates and keep the gene with the highest read count total? What is the best practice

edger

updated 8.3 years ago • es874

do the two class (unpaired) SAM analysis between two groups of ratios: group1: C1/C2 and C3/C4 (duplicates) group2: C5/C6 and C7/C8 (duplicates), How can I get the ratio of two columns of an AffyBatch file? and how to make the result

updated 20.1 years ago • Flora Fan

set that came from cytokine membranes. Each membrane contains 23 specific cDNA fragments spotted in duplicates. The experiment design includes two treatment of interest, stimulant (pre-activated or non-activated cells) and...on each membrane, I like to run limma as factorial design. My question is how I should handle the duplicate spots (block effect) in limma processing? Thanks! JP- </div

Normalization limma Normalization limma

updated 19.8 years ago • Jianping Jin

data.frame", function(from) as.data.frame(from)) as.data.frame.Vector <- function(x, row.names=NULL, optional=FALSE, ...) { as.data.frame(x, row.names=NULL, optional=optional, ...) } setMethod("as.data.frame", "Vector", function...x, row.names=NULL, optional=FALSE, ...){ x <- as.vector(x) a…

S4Vectors methods

updated 5.5 years ago • Aditya

I have complete mirdeep2 on my 15 samples. Results included several duplicates but the read counts differed. I have done a lot of research but there is nothing concrete on how to handle duplicates

deseq2 mirdeep2 microRNA differential expression analysis

updated 4.9 years ago • ljbond

Hi everyone, I am sorry to ask another question, however, there is an error message that keeps me puzzled. When passing over a list of human entrez IDs to reactomePA for GSEA using <pre> result <- gsePathway(anaData, nPerm=10000, pvalueCutoff=0.2, pAdjustMethod="BH", verbose=FALSE)</pre> Rstudio becomes busy and cannot finish computation. When I manually stop it I get the e…

reactomepa reactome gsea fgsea

updated 6.7 years ago • martin.busch

preformatted">Dear Bioconductors, I am working with an array containing 17496 probes spotted in duplicate. To deal with duplicate spots I used duplicateCorrelation like this: cor<-duplicateCorrelation(MA,ndups=2, spacing...but after duplicateCorrelation the middle one is missing while the two other ones are there in duplicates. This leaves me clueless... Any idea? Best, Georg --…

updated 20.1 years ago • Georg Otto

P VALUE META ANALYSIS, are duplicate markers from multiple studies not accepted? I am conducting a p value based meta analysis with GWAS summary statistics...WARNING: Invalid p-values for 8 other markers also ignored WARNING: An additional 87 rows with duplicate marker names were ignored Does METAL not accept same markers from multiple studies with a different p value and

metaanalysis metal gwas

updated 2.3 years ago • Ymberzal