Bioconductor Forum

how do I tell R which samples I am interested in comparing to which other samples? I have two duplicate experiments that are vector controls, two duplicate experiments that are virally transfected, and one experiment

Normalization Normalization

updated 22.3 years ago • Michael Benjamin

zero In addition: Warning message: Samples have been merged or lost during counting. Check for duplicate bam files. sessionInfo( ) R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux

DiffBind

updated 18 months ago • Mark

Hello All, I am trying to implement LIMMA room duplicate correlation strategy for my RNA-seq samples using blocking setup. I need to consider following points into account

limma limma voom duplicatecorrelation

updated 8.0 years ago • alva.james

bitr function from Ensembl to Symbol,  the number of genes is also 22142, however, it contains duplicates.       After removing duplicates, the number of genes is 22103. I don't know why it happened. Any help will

clusterprofiler

updated 6.3 years ago • tenger929

prog scores and ranks for All 15 samples, with patient duplicates) ###pearson### age<-c(33,28,37,41,38,37,33,33,28,36) ###spearman### age.rank<-c(2,1,4,6,5,4,2,2,1,3) ###################################################################### ############################## COR_3<-rep(NA,19992) COR_4<-rep(NA...id<-rank.neg.2 ### heat map ht.dat<-as.dat…

updated 11.1 years ago • Helen Smith

while ago I asked how to treat 3 samples per individual (ID) in a DESEQ2. It was recommended to use Duplicate Correlation in limma. I wonder how to combine both packages: I run my DESEQ2 with dds0 <- DESeqDataSetFromMatrix...colData, design = ~ AGE+ DIAGNOSIS + SEX) I see that the duplicate correlation is run with dupcor <- duplicateCor…

DESeq2

updated 2.5 years ago • Bine

gene symbols as rows in my expression matrix, thus I can't match the different EnsemblIDs. If I keep duplicates this would be a sort of *increased weight* for the considered genes, leading to a slightly skew distribution for...the enrichment scores. Is it safe to delete duplicates or am I losing relevant information

msigdb GSEABase GSVA

updated 3.0 years ago • forlani.luca

vs healthy? Can duplcateCorrelation be applied with block=subject tissue? Should one of the duplicate pairs be removed based on some QC measure? Is there some way to combine the data from the duplicate pairs of fastq

limma duplicateCorrelation

updated 5.9 years ago • richard.vinisko

from the biological replicates. Here come and my questions. 1. How shell I treat my technical duplicates in term to compare them with biological duplicates. Any example code or link to such will be greatly appreciated...2. Having only duplicates (technical or biological) am I allowed to use t-statistics (equal variance) with webbioc/multtest or I can use only

Microarray webbioc Microarray webbioc

updated 17.8 years ago • jane janes

pAdjustMethod="fdr", seed=TRUE, by="fgsea") Fehler in .stopf("Duplicate values in %s not allowed", universeArg) : Duplicate values in names(stats) not allowed Zusätzlich: Warnmeldung: In preparePathwaysAndStats

GSEABase

updated 7 weeks ago • Sidra.Gull

cannot contain duplicated sequence names</pre> --- It's quite clear that there must be some duplicates either in the bam file or in the exonsBy object. However any combination of duplicates(ebg), which(duplicates(names...ebg)), etc. that I could try returned no duplicate. => __hence my question__ : how to narrow down the search on which object is duplicated ? * in particular, w…

software error

updated 7.0 years ago • c.legrand

<div class="preformatted">There are times when it makes sense to have genes duplicated in both the universe and the set of interest - e.g. if the geneIds come from BLAST hits of unigenes of an unsequenced species against the genes of a sequenced species. I fiddled a bit with GOstat, but was not able to see how to change the code to allow this. (I can see where duplication was removed in t…

updated 17.5 years ago • Naomi Altman

<div class="preformatted">Dear group, Is there any place where I can get all the unique probe ids for all the Affy human chips (~13 chips). I am trying to get the unique probes (no duplicates). It turned out to be very computing intensive problem. I took all the probes from all 13 chips and made a program that...unique probe ids for all the Affy human chips (~13 chips). I am trying to get …

Annotation hgu133a2 affy Annotation hgu133a2 affy

updated 20.5 years ago • S Peri

in 2, and  the alignment 2 in pair 1 is identical to the alignment 1 in 2, are also treated as duplicates). Thanks

alignment duplicate

updated 8.2 years ago • Frocha

div class="preformatted">Hi Ian and everybody, The problem of PCR duplicates cannot be elegantly solved from the output of the sequencer. It has to be solved at the bench. That is why I believe...wrote: > Thank you for your response Ivan! > > I completely agree that removing duplicates is a necessary step for peak calling. > > I seems as though keeping dupli…

Coverage Kidney DESeq Coverage Kidney DESeq

updated 13.4 years ago • Ivan Gregoretti

wrote: > > >On a different note > > >The arrays I have tested LIMMA on have 2 duplicates and are spaced evenly > > >throughout the array and so have no problems running your functions. > > > > &gt...else at the Sanger Insitite would like to be able to use LIMMA > but > > >the…

limma limma

updated 21.4 years ago • Gordon Smyth

of differential expression occurs in this experiment, > the very close similarity between the duplicates compared to the > other conditions leads me to thing that these duplicates were either > not biological replicates...or the duplicates were processed together > causing correlation. I know that the replicates are biological replicates, so I think...very likely that…

Normalization affy limma affyPLM PROcess Normalization affy limma affyPLM PROcess

updated 19.2 years ago • Matthew Hannah

Hello, I have some gene expression data for different tissue types with multiple replicates. My species has undergone a historical duplication event and and I am looking to compare the genome copies to identify which one is more highly expressed. Due to the...data for different tissue types with multiple replicates. My species has undergone a historical duplication event and and I am looking to …

stats r RNASeqData limma voom

updated 16 months ago • pl23

180), 1year(365), 2years(730)) between my wild type and knockout mouse models which I have in duplicates for each time point. So, I have 2 knockout  and 2 wild type mice for each time point. I analyzed my data using DESeq2...as follows: > countdata <- read.table("~/desktop/counts\_table\_lungs.txt", header = TRUE, row.names = 1) > library(DESeq2) > countd…

deseq2 timecourse

updated 7.4 years ago • uu2110

available [here](https://github.com/nrode/readVcf/raw/master/file.bgz)) and it seems that `` readVcf `` duplicates some of the rows in the output vcf. Here is an example: library(VariantAnnotation) <code>## Defines the positions of...which might mess things up, but I would expect only two rows still. Is-there a way to avoid this duplication or alternatively to remove …

variantannotation readvcf

updated 8.9 years ago • nicolas.o.rode

T, file = "intensity.txt", pd=targets, filterXY = F) Run champ.CNA Error in read.table(file, row.names = T, sep = "\\t") :   invalid 'row.names' specification   Clearly "row.names= T" is causing the problem. Could you fix this

ChAMP

updated 8.8 years ago • yuping.zhang

Hi all. After a lengthy struggle (I am a beginning student), I was able extract a list of genes from one GSE which contained 25 GSMs. From this GSE, I extracted a list of gene symbols after which I removed all of the duplicates. So, I am now assuming that the gene symbols I obtained are from all of the GSMs within that GSE? If so, I am attempting to perform the same operation on six additional G…

GEOquery CancerData limma RCy3 CancerInSilico

updated 3.3 years ago • Caitlin

div class="preformatted">Dear list, I have an array with duplicate spots that are not evenly spaced. The help for duplicateCorrelation indicates that the spots should be spaced...using the spacing argument. I'm wondering if I can order the rows of my MAlist such that the duplicate spots are on evenly spaced rows and then run duplicate correlation. What I have done is below. Is reordering …

updated 16.2 years ago • Scott Ochsner

limma results while it doesn't have any column show rawnames(ID\_REF). when I use the argument "row.names = TRUE" I get this error: Error in write.table(tab, file = file, quote = FALSE, row.names = FALSE,  :    formal argument...row.names" matched by multiple actual arguments I will be really grateful if someone help me to resolve my problem.  Thank

limma

updated 8.8 years ago • moradzadeh_k921

Hello everyone, I am trying to run a differential expression analysis with duplicates, but do I get this warning message any suggestions? # Create identifiers for case-control status Group <- factor...weights already in the data object: w <- matvec(MA_norm$weights,aw) # Account for duplicate spots dupcor <- duplicateCorrelation(MA_norm,desig…

limma microarray cancer

updated 4.9 years ago • everardoremi

However, I have a doubt and a problem. Doubt: My genes are spoteds two times in the membrane (in duplicate). I generated the file of data with all of the duplicated genes, 7680 spots. When I executed the command maM(ka.susc.norm...verify that the genes continued duplicated. I ask: Should I must get the average among the two genes (duplicates) before normalizing them? Or does the tool marray dete…

Normalization limma Normalization limma

updated 21.4 years ago • Marcelo Luiz de Laia

I'd like to use Rsamtools to remove duplicate reads from a bam file. I'm looking for a solution similar to samtools markdup -r -s in.bam out.bam. Can anyone tell me

Rsamtools

updated 2.1 years ago • Adnan

read.metharray] Instantiating final object ... Error in data.frame(numeric(n), row.names = nms) : duplicate row.names: 200517420015_R03C01, 200517420102_R06C01 Calls: read.metharray ... annotatedDataFrameFrom

minfi illumina450k methylation

updated 8.4 years ago • hrishi27n

I'm a little confused about the way you're calling the 'lmFit' function. Your arrays appear to have duplicate spots, but you have the correlation as zero. Something is very wrong with your arrays if there is zero correlation...between the duplicate spots! I suggested you read the limma vignette very closely, especially the sections on common reference designs...gt;library(limma) >targets &…

Normalization limma oligo Normalization limma oligo

updated 18.3 years ago • Jenny Drnevich

vcf) none geom is used Error in data.frame(seqnames = as.factor(seqnames(x)), start = start(x), : duplicate row.names: rs7410291, rs147922003, rs114143073, rs141778433, rs182170314, rs115145310, rs186769856, rs77627744

ggbio

updated 8.8 years ago • kevin.rue

re not working properly. The new variable has its values mixed up, and they do not correspond to its row.names. # Generate the first dataframe data1 <- data.frame(height=rnorm(20,3,0.2),width=rnorm(20,2,0.5)) # Sample a smaller dataframe...Bind the new variable to data2 data2 <- cbind(data2, color) # Merge the data1 and data2$color by row.names, and force it to has the same values …

updated 13.4 years ago • João Daniel Nunes Duarte

name of genes into \*.csv file but with name of genes ? <pre> write.csv(highly_variable_lcpm, row.names=y2$genes, file = "highly_variable_lcpm_genes.csv")</pre> I get error message as below <pre> Error in write.table(highly_variable_lcpm...row.names = y2$genes, file = "highly_variable_lcpm_genes.csv", : invalid 'row.names' specification</pre> How to solve the problem

edgeR lcpm bioconductor

updated 6.9 years ago • Björn

<div class="preformatted">Hi all, I have a logical index matrix now and need to create a two column matrix that contains the row.names and col.names of this matrix where the logical index is TURE. The logical matrix is like this: Gene2 Gene1 Gene3 Gene1...Hi all, I have a logical index matrix now and need to create a two column matrix that contains the row.names and col.names …

updated 15.0 years ago • aiguo li

there is no normalization step required, as it is already normalized). 3. The gene ids had some duplicates, i removed the duplicates by taking the entries with max expression values, is this the right way to do it. 4. Should

WGCNA Normalization RNASeq

updated 24 days ago • Vishnu

suggestion regarding a  package I could use for annotating the structural variants (especially duplications, inversions, translocations). Many thanks,   -- bogdan   &nbsp

vcf

updated 8.5 years ago • Bogdan

and most important: the BAM file I obtained from this code line does not contain by default any duplicate reads >>> I knew this by counting the PCR duplicates in the file but was 0 using this command samtools view -c -f...1024 file.bam Am I right that in such file, no duplicates are there ? when I triled to rerun alignment but including the command --outSAM…

RNAseq123 VariantFiltering Alignment VariantAnnotation

updated 2.4 years ago • Mohamed

Does anyone have any ideas? ```r countdata.P1=read.csv("all.p1.count", sep="", head=T, skip=1, row.names = "Geneid") # ignores first line rawdata.P1=countdata.P1 # Clean file names colnames(countdata.P1) <- gsub("\\.Aligned.sortedByCoord.out.bam...empty sample, and G05 - not enough counts write.table(countdata.P1, "counts_cleaned.txt", sep="\t", row.names=FALSE, quote=FALSE) rn…

dese DESeq2

updated 2.8 years ago • lmrogers34

can I create a PHENO_DATA for command: countData <- as.matrix(read.csv("gene_count_matrix.csv", row.names="gene_id")) colData <- read.csv(PHENO_DATA, sep="\t", row.names=1) Thanks in advanced

RNASeq RNASeqData RNASeqRData

updated 2.5 years ago • marymshahi2021

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20050922/ 0f274019/attachment.pl

updated 19.5 years ago • Hoen, P.A.C. 't HKG

Hi everyone. What is the best way to reproduce MAS 5.0 outcome for each probe pare intensity value using BioConductor? I tried bg.correct.mas() function alone, but it did not seem to work for me, although resulting P value of a probe set is kind of close the absolute call is way off. Any suggestions? Thank you very much Dmitry N. Grigoryev, M.D., Ph.D. Data Analyst Gene Expression Profiling …

probe probe

updated 22.0 years ago • DMITRY GRIGORYEV

If I ask for the chromosome location of the start of geneID 5004, I get: > get ('5004', org.Hs.egCHRLOC) 9 116125123 But geneID 20 gets me two identical values: > get ('20', org.Hs.egCHRLOC) 9 9 -139021506 -139021506 I noticed this after using toTable to create a data.frame from this environment: I get two identical rows for geneID 20: > subset (toTab…

updated 16.0 years ago • Paul Shannon

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070105/ be5f20df/attachment.pl

updated 18.2 years ago • Vinoy Kumar Ramachandran

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070607/ e761e0f8/attachment.pl

updated 17.8 years ago • Mcmahon, Wyatt

I was searching the archives for the warning message I got with duplicateCorrelation. I got that resolved but found this comment from Gordon from last November. "Secondly, assigning zero weight is not the way to remove missing or control spots. You should leave the weights as they are are and instead subject the data object. For example, isBlank <- (MA$genes$Status %in% c("blank","miss")) …

limma weaver limma weaver

updated 19.8 years ago • lepalmer@notes.cc.sunysb.edu

for adjusted copy ratio (CR), such that CR < LO is called a deletion and CR > HI is called a duplication? &nbsp

PureCN copy-ratio threshold

updated 6.4 years ago • twtoal

<div class="preformatted"> Hi I have a 6 slide experiment I'd like to be able to plot a MA plot that combines the data from all six slides and takes in to consideration duplicates on the slides I'm currently trying variations of the command as outlined on page 9 of the Limma users guide M <- fit...be able to plot a MA plot that combines the data from all six slides and takes in to…

limma limma

updated 21.5 years ago • Jason Skelton

div class="preformatted">Dear list, I have this 8 affy arrays under 2*2 factorial design, with duplicates under each condition. The RNA degradation plot worries me since the slopes from 8 arrays are so different, with...duplicates under each condition as one group (see the QC plots at http://cactus.salk.edu/temp/QC-1.jpeg) I would suspect that

affy affy

updated 19.2 years ago • Fangxin Hong

div class="preformatted">Hi I am using maanova and have duplicate spots on my array. I want to collapse these duplicates after rlowess transformation. In the April 25 2008 Manual

Genetics maanova Genetics maanova

updated 16.9 years ago • Cecilia McGregor

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: >&gt...non-unique values when setting 'row.names': >> >> I have tried to run the same script…

updated 11.4 years ago • Gordon Smyth

NormE.final <-NormE.final[order(NormE.final$genes$Name), ] NormE.final$genes$Name # calculate duplicate correlation between the 2 replicates on each array corfit <- duplicateCorrelation(NormE.final, design, ndups...the correlations boxplot(tanh(corfit$atanh.correlations)) # fit the linear model, including info on duplicates and correlation fit <- lmFit(NormE.final, design, …

updated 13.6 years ago • bigoun

that 10X barcodes are reused and before I added the sampleIDs to the column names I did have duplicate barcodes. So my question is, how should I deal with merging the reads for these three samples? Will it suffice to just...omit the batch ID from the column names as they stand, which would leave duplicate column names/cell IDs? If so, I assume that Scater and downstream Bioconductor packag…

SingleCell SingleCellExperiment scater

updated 4.1 years ago • camerond

Hi everyone: I have list of overlap hit index in IntegerList where some duplicated index exist. I have tried of using `` unique, ``or `` duplicated ``method from `` IRanges ``packages, but duplication can't be removed anyway. Removing duplication for GRanges object is different from IntegerList. However, I tried other way like such as coercing IntegerList to integer vector then use `…

r iranges integerlist

updated 8.4 years ago • Jurat Shahidin

WT B was also done in triplicate using a different method. The slides are 7.5k oligos spotted in duplicate ( the duplicates are in the same block 10 rows below the first copy), although there are control genes which appear

limma limma

updated 21.4 years ago • Pete

<div class="preformatted">At 05:30 AM 11/02/2005, Hua Weng wrote: >Dear Dr. Smyth and Bioconductor members: > >I have a question about M Values in toptable in LIMMA package. I know the >M in toptable is not a simple average from all the replicates, it is a >coefficient value from lmFit. I have three biological replicate array >and within each arra…

limma DOSE limma DOSE

updated 20.1 years ago • Gordon Smyth

lt;- MouseRNAseqData() test <- df_genes@assays$RNA@data # a Seurat dataset shared_markers <- row.names(mrnaseq)[row.names(mrnaseq)%in%row.names(test)] # shared markers in the reference and in our gene expression data sub_test

SingleR SingleCell

updated 2.6 years ago • amit.korngut

of defeat. Inspired by the help file for read.targets(), I am trying to borrow the argument row.names from the function read.data() > targets=read.targets(infile="Targets_T0.txt", row.names=1) to no avail, as I may be...than the number of columns, the first column in the input is used for the row names. Otherwise if row.names is missing, the rows are numbered. Using row.names = NULL forc…

Agi4x44PreProcess Agi4x44PreProcess

updated 15.9 years ago • Massimo Pinto

gt; df2<- as.data.frame(mynormSPN) > merged_panNET_SPN<- merge(df1, df2, by.x="row.names", by.y="row.names") > rownames(merged_panNET_SPN) <- merged_panNET_SPN[,1] > merged_panNET_SPN[,1] <- NULL ``` ``` > tmerged_panNET_SPN...gt; annoGEO<- merge(PD_panNET_SPN[,c(1,3)], tmerged_panNET_SPN, by.x="Sample_Name", by.y="row.names",…

methylationArrayAnalysis ChAMP MethylationArrayData

updated 3.7 years ago • FWNL15

analysie with specific coloums### library('DESeq') x=read.delim("readcount.xls",row.names=1) x=round(x[,1:4]) group=factor(c("A","A","B","B")) cds <- newCountDataSet(x, group) cds <- estimateSizeFactors(cds) cds <- estimateDispersions...a<-subset(res,padj<0.05) dim(a) write.table(a[,1],"each.txt",quote=F,col.names=F,r…

updated 11.3 years ago • Guest User

Hi list, The probe package for rae230b on the bioconductor metadata page, appears to be a duplicate of the probe package for rae230a. Is this a typo in the filename, or is it the wrong file, or am I missing something? Does

rae230a rae230b probe rae230a rae230b probe

updated 20.9 years ago • Caroline Johnston

div class="preformatted">The selected gene list contained duplicate ids. I'm pretty sure this is the problem. The Category + GOstats code should detect such input errors and give a sensible

GOstats Category GOstats Category

updated 18.3 years ago • Seth Falcon