Bioconductor Forum

Hello, I have some questions about running a likelihood ratio test in the DESeq2 package in R. My experiment has two factors: sex and population, with 8-12 replicates per condition. I wish to identify...nbsp; countData <- read.table ("Counttable.txt", header=TRUE) stickleDesign = data.frame ( row.names = colnames(countData), sex = c("M", "F", "M", cont... ) pop = c("A", "A…

deseq2 LRT differential gene expression

updated 10.0 years ago • newsomew13

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 6.2 years ago • Aditya

3.052927 comp364180_c1_seq1 501.804 177.331 826.277 4.660 2.220 0.000004 0.002997 2.220183 DESEQ2 id baseMean baseMeanA baseMeanB log2FoldChange lfcSE pval padj "real" log2FC comp587382_c0_seq1 64.669 13.909...501.804 177.331 826.277 1.924 0.299 0.000000 0.000000 2.220183 [] library(DESeq2) data = read.table("counts.matrix", header=T, row.names=1, com='') col_orderin…

DESeq DESeq

updated 11.4 years ago • Kuenne, Carsten

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 10.6 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 8.6 years ago • ZheFrench

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 19.8 years ago • Steffen Neumann

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 16.3 years ago • Amit Kumar

Hello, First, I know that DESeq2 is not meant to be run without replicates and results will not be meaningful. However, I have replicates (n=>30) in one...while another group (T) has only a single sample. This is the requirement of the project. I run the DESeq2 without any error and I found a change in the expression of ~9000 genes (padj < 0.05). I am sharing the script and don't if…

DESeq2 rnaseqGene DifferentialExpression GeneExpression

updated 4.5 years ago • SUMIT

Hello, I am analyzing a large cohort (1000+ samples) for differential expression analysis. I am using Deseq2 to process raw counts from  samples correcting by two confounding factors (namely sex and histology origin). As output we obtain a shortlist of interesting candidates with strong adjusted p-value (e.g. p < e-14) and would like to plot the result so that I can visua…

deseq2 limma differential expression visualization

updated 7.5 years ago • Mbosio85

from three different batches (PK, GB, and EG) and I am trying to apply batch correction using DeSeq2. I am intersted in contrasting all three condtions (i.e. A vs B, B vs C and A vs C) while taking the batch effect into account...3)))) (batch <- factor (c("PK","GB", "EG","PK","GB", "EG","PK","GB", "EG"))) # Analysis with DESeq2 ---------------------------------------------------- li…

deseq2

updated 6.8 years ago • pkhadka

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 9.0 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 22 months ago • rae.alshammari

Hi, I am writing a table of DESeq2 results in the following way and just wondering how to easily write to two separate tables based on the LFCs below...Hi, I am writing a table of DESeq2 results in the following way and just wondering how to easily write to two separate tables based on the LFCs below: summary.DESeqResults...write.table(treatment_pw_padj.001_sorted,"treatment_pw_padj.001_so…

deseq2

updated 6.2 years ago • rbronste

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 11.3 years ago • Jens Preussner

Using paired data, I am comparing the lung microbiome with the mouth microbiome in 33 patients I used deseq2 just fine with this, however when I did it in 8 patients comparing the lung microbiome over two time points (again paired data) I got this error: log2 fold change (MAP): time later vs baseline  Wald test p-value: time later vs baseline  DataFrame with 0 rows and 6 …

deseq

updated 9.6 years ago • l.weissenburgermoser

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 7.2 years ago • spollack

``` This is my code :- library(DESeq2) library(ggplot2) countData <- read.csv('/home/keshav/Downloads/gene_count_matrix.csv', header = TRUE,sep = ",") countData <- as.matrix(countData) rownames(countData) <- countData[ , 1] countData = as.matrix(countData[ , -1]) head(countData) (condition <- factor(c("Normal","Tumor","Normal","Tumor"))) (coldata <- data.frame(…

DifferentialExpression

updated 3.5 years ago • srikar

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 13.7 years ago • Angela McDonald

Hi, maybe I am doing something wrong but I cannot find a log2FoldChange inside the results of DESeq2: res = results(dds, contrast=c("cond", test, control)) dRes = as.data.frame(res) dRes$log2FoldChange[1] [1] 12.62795 dRes[dRes$log2FoldChange...pvalue </code> [6] padj <0 rows> (or 0-length …

deseq2

updated 8.5 years ago • ribioinfo

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 7.4 years ago • Gurkenkönig

Hello! I am running DESeq2 on a dichotomous outcome (77 no, 41 yes). My concern, is that I am getting an enormous number of counts labeled as low. I've...Hello! I am running DESeq2 on a dichotomous outcome (77 no, 41 yes). My concern, is that I am getting an enormous number of counts labeled as low. I've been...outcome. I have 20338 genes.  Code:  `` data<-read.csv("T…

deseq2 low count genes

updated 8.0 years ago • hs.lansdell

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 10.9 years ago • amrahweijn

Hello' I have an error of ncol(countData) == nrow(colData) is not TRUE when I tried to set matrix. Code is below: countdata = read.table('k.txt', header=TRUE, sep = "\t", row.names = 1, as.is=TRUE) show(countdata) countdata <- as.matrix(countdata) head(countdata) condition <- factor(c(rep("x", 2), rep("y...I tried to set matrix. Code is below: countdata …

deseq2

updated 6.4 years ago • trumbia

<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 19.8 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 21.5 years ago • Jakob Hedegaard

I'm trying to perform RNASeq analysis with DESeq2 in RStudio, and as one of the quality control steps I am trying to perform Principal Component Analysis on my DESeq2...object. I've included the code chunk below - I am able to create the DESeq2 object just fine, but run into problems plotPCA(). I think there's an issue with the packages talking to each other/masking...each other, but I'm not sure…

deseq2 pheatmap RColorBrewer BiocGenerics

updated 5.6 years ago • matthewzli777

<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 18.7 years ago • Gordon Smyth

problem reading in a CSV file (hope this is an appropriate forum as it is for use directly with deseq2!) I am reading in a CSV count matrix, with first column as gene names. I am trying to make the first column a rownames columns...1\] rownames(countdata1)<-countdata1\[, 1\] I get the following error:  duplicate 'row.names' are not allowed I have tried so many ways …

deseq2 countdata

updated 7.9 years ago • A

Hi, I am trying to run DESeq2 with the duplicated raw counts from 4 groups and 2 conditions using the  two-way ANOVA design below. Referring...Hi, I am trying to run DESeq2 with the duplicated raw counts from 4 groups and 2 conditions using the  two-way ANOVA design below. Referring a...vignette of DESeq2, various comparisons have been run as below. Besides of these results, I…

deseq2 results

updated 10.3 years ago • jjinhyoungkim

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 16.7 years ago • Vishal Thapar

Hi, I am using DESeq2 to find Differentially expressed genes. I am using the following code: <pre> conds<-c("kd1","kd1","kd2","kd2","GFP","GFP") Design&lt...data.frame(condition=conds,row.names=paste(conds,rep(c(1,2),3),sep="_")) dds <- DESeqDataSetFromMatrix(countData = assay(se), colData = Design, design…

deseq2 rnaseq differential gene expression

updated 9.3 years ago • ta_awwad

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 3.4 years ago • sharvari gujja

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 5.9 years ago • Brian Smith

182). However, when I am trying to do DE, I cannot prepare the data for dds command to kick off the DESeq2 commands. I don't know what the problem is, but I get some errors while I looked for them on the internet and even went over...the DESeq2 tutorial and other examples. It might be noteworthy to declare that I do not have the raw htseq count data and I tried...I also attached my colData to …

DESeq2

updated 4.9 years ago • Pedram

I'm using DESeq2 to analyze 7 patient-matched samples (*1 tumor and 1 normal from each patient*) and I want to identify DEGs with padj&lt...I'm using DESeq2 to analyze 7 patient-matched samples (*1 tumor and 1 normal from each patient*) and I want to identify DEGs with padj<0.05 and LFC>2 in Tumor compared to Normal. I have annotated my coldata file to include a column for "Sour…

DESeq2

updated 4.5 years ago • rln0005

Hi, After DESeq2 analysis of my RNAseq data  in order to obtain differentially expressed genes between 2 cell types, I have a csv...is the following, although I am not sure if it is correct: d <- read.csv("myfile.csv", header=T, row.names=1) all\_genes <- row.names(d) DE\_genes <- all\_genes\[which(d$padj<0.05)\] head(DE\_genes) I will really appre…

goseq DESEQ2 RSTUDIO CODE

updated 10.2 years ago • amyfm

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 16.9 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 11.2 years ago • Anna N.

per condition). Reads are paired-end, 100 bp. I performed differential expression analysis using DESeq2 and was surprised not to find a gene as significantly differentially expressed (it has been reported in an array and...another RNASeq experiments studying the same conditions-but different samples). Here is the DESeq2 procedure I followed: library("DESeq2") DataFrame=data.f…

deseq2 differential gene expression

updated 9.8 years ago • Jane Merlevede

Hello Mike, please kindly advise on the following question regarding analysis with deseq2. This might be a very general inquiry about running deseq2 with a continuous variable, but the characteristic of this...Hello Mike, please kindly advise on the following question regarding analysis with deseq2. This might be a very general inquiry about running deseq2 with a continuous variable, but the char…

deseq2

updated 5.7 years ago • jasminelee0603

are in C:\\Users\\Administrateur\\AppData\\Local\\Temp\\Rtmps76hIZ\\downloaded\_packages library(DESeq2)\# again I had an error Error: le package ‘S4Vectors’ nécessaire pour ‘DESeq2’, mais est introuvable \#In addition: Warning message...R-3.5.1/library/S4Vectors/DESCRIPTION', probable reason 'No such file or directory' remove.packages('DESeq2') \# i tried to remove deseq2 and install it…

deseq2 S4Vectors

updated 7.1 years ago • roghaiyeh.safari

Hi, I am performing differential expression (DEG) analysis using DESeq2. I have no replicates, and I understand that without replicates, it is useless to conduct this analysis. However, I have...suggestions? It will be great helpful for me to complete my work # Load required libraries library(DESeq2) # Read in the count data count_data <- read.csv("count.csv", header = TRUE, row.names …

DESeq2

updated 14 months ago • kuttibiotech2009

ways that I believe should be basically equivalent, I get very different results. When I run DEseq2 using the design formula __~ group__ (as illustrated on p. 24 of the Oct 13, 2015 manual, where group is a combination of...library("edgeR") #read in count matrix counts = read.csv("combined_counts.csv",header=TRUE,row.names=1) #filter counts to remove low reads noint = rownames(counts) %i…

deseq2 differential gene expression rna-seq

updated 10.1 years ago • erin.gill81

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 3.3 years ago • Jiayi

Hello everyone, I am using Deseq2 to perform differential gene expression between 2 groups (each 14 samples) using the following code: ep<-read.table...counts.txt",header = TRUE, row.names = 1)  cp<-read.csv("Annotation.csv") dds <-DESeqDataSetFromMatrix(countData = ep,colData = cp,design =~Response

outliers deseq2 logfoldchange

updated 7.9 years ago • lirongrossmann

to coding on Rstudio. I'm doing a RNA seq analysis to test for differential gene expression using deseq2, by using unpaired samples. I just wanted to know if I altered the following script template correctly to indicate...count table countdata <- read.table("family_13_01_revised_RNA-seq.counts_fixed.txt", header=TRUE, row.names=1) # Remove .bam or .sam from filenames colnames(co…

deseq2 rnaseq

updated 6.3 years ago • adeler001

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 18.5 years ago • Ian Roberts

difference? The script I used is below. I am relatively new to R and have even less experience with DESeq2. I appreciate any thoughts! Code should be placed in three backticks as shown below ```r gene_counts <- read.csv("gene_count_matrix.csv...header = TRUE, row.names = 1) study_countsLabels <- read.csv("col_data.csv", header = TRUE, row.names = 1) colData <…

DESeq2

updated 22 months ago • hmillike

D-xylulose-5-phosphate … 557 722 303 700 935 507 275 594 694 2 Following the DESEq2 tutorial https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#indfilt I have...package="pasilla", mustWork=TRUE) cts <- as.matrix(read.csv(pasCts,sep="\t",row.names="gene_id")) coldata <- read.csv(pasAnno, row.names=1) coldata &a…

deseq2 dataframe pasilla

updated 6.7 years ago • ecg1g15

Dear community, a quick question on how fold changes are calculated in DESeq2. Below I have the counts for a gene X in 5 treatments and a control, with 4 replicates: Control : 1 0 0 0 Treatment 1: 1 3 475 0...Dear community, a quick question on how fold changes are calculated in DESeq2. Below I have the counts for a gene X in 5 treatments and a control, with …

DESeq2 RNASeqData

updated 4.6 years ago • GlycineMax

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 18.0 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 9.7 years ago • lucia.caceres

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 5.7 years ago • ljbond

I am writing to inquire about a problem I keep running into while running DESeq2. After running DESeq2 comparing two samples, I encounter an issue where I get >10000 differentially expressed genes...row.names= F) > > # Change naming scheme in notepad++ > > countData <- read.delim("countsonly.csv", row.names = 1, header = TRUE, sep...…

deseq2

updated 5.3 years ago • anjali_mohan

I am a new learner of DESEQ2 and have seen similar posts on this forum but could not find clear answers. What would be the best way to create heatmaps...I am a new learner of DESEQ2 and have seen similar posts on this forum but could not find clear answers. What would be the best way to create heatmaps specifically with 2 log fold change(base 2) in DESEQ2 or R in general? In DESEQ2, heatma…

DESeq2

updated 2.4 years ago • bio2249

Morning! I've just run DESeq2 on my RNAseq data with a dichotomous outcome, and I'm getting results that mean I have absolutely no deferentially...Morning! I've just run DESeq2 on my RNAseq data with a dichotomous outcome, and I'm getting results that mean I have absolutely no deferentially expressed genes... My input is a count matrix with samples in columns and genes in rows, i.e:   …

deseq2 adjusted pvalue

updated 8.1 years ago • hs.lansdell

Hi, I am trying to annotate a list of differentially expressed genes output by DESeq2, with ensembl IDs, gene symbols and gene descriptions. I originally aligned and mapped the reads using a .gtf annotation...file from NCBI, so the DESeq2 gene list appears to have a list of Entrez gene ID and locus tags as identifiers. I constructed the biomaRt query below...b # [1] ensembl_gene_id entrezg…

biomaRt

updated 2.7 years ago • alan.g.hudson

Hi, I performed analysis using old 1.14 version of DESeq2. I had to repeat such analysis now with version 1.24. I've received very different results. With 1.14 I've received 63...Hi, I performed analysis using old 1.14 version of DESeq2. I had to repeat such analysis now with version 1.24. I've received very different results. With 1.14 I've received 63 hits...de_results) write.table(as.data.fra…

deseq2

updated 6.0 years ago • michalina.marija

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 16.7 years ago • Jenny Drnevich

div class="preformatted">Hi, I used DEseq2 v. 1.3 under R-devel because I have many different values for my design (celltype) and it worked ok. I upgraded my libraries...not working. Might this be a bug? > exp.data<-read.table("./count_table_by_gene.txt",header=T,row.names=1) > exp.ann<-read.table("./desc_colonnes.txt",header=T) > genex<-DESeqDataSet…

DESeq2 DESeq2

updated 11.8 years ago • Sylvain Foisy