Bioconductor Forum

Hello, I am trying to use the Bioconductor DESeq2 package but I keep running into errors. I wanted to reach out and ask for any advice on how to fix my code to use the DESeq2...Hello, I am trying to use the Bioconductor DESeq2 package but I keep running into errors. I wanted to reach out and ask for any advice on how to fix my code to use the DESeq2 package. The error message that I keep ge…

DESeq2 Bioconductor

updated 3.8 years ago • Kevin

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 6.7 years ago • Yasavoli.h

Dear All,  I have an RNA seq experiment with 5 different cell types (=my 5 conditions are the 5 cell types), and I would like to identify those genes that show differential expression between at least 2 cell types (so basically like performing an ANOVA). I am a medical doctor and new to R with very basic knowledge in statistics so I would like to be sure that my code is correct…

deseq2 rnaseq statistics

updated 9.5 years ago • kissmatee

or INFL3 against TCR+INFL3. It implied creating 4 different counts and metadata files and running DESeq2 4 times. Alternatively, I run all samples at once (in a single DESeq2 run) and extracted the desired contrasts with the...lt;- subset(my_results, padj < 0.05) write.table(resSig, file_name, sep = '\t', quote = F, row.names = F) } ``` When DE results are filtered using a corre…

contrasts DESeq2

updated 2.6 years ago • jovel_juan

shrinkage should make log2foldchange from DESeq2 be simply equal to (mean of normalized counts group B) / (mean of normalized counts group A). However, it seems that some degree...2]. All preprocessing steps are copied from the official guide. Result: log2Foldchange from DESeq2 without fold change shrinkage is not identical to what is calculated from normalized count matrix. And sign inversion.…

DESeq2

updated 4.9 years ago • Yanling

Is there a way to make a heatmap using DESeq2 for paired data? I am comparing the lung microbiome with the mouth microbiome in 33 patients And also comparing...Is there a way to make a heatmap using DESeq2 for paired data? I am comparing the lung microbiome with the mouth microbiome in 33 patients And also comparing the lung microbiome over two time points (again paired data). …

deseq2 heatmap

updated 9.6 years ago • l.weissenburgermoser

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 20.8 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 20.4 years ago • jsv@stat.ohio-state.edu

normalization techniques to account for batch effects on an RNAseq dataset.  I am using DESeq2 for DE analysis, and RUVseq for normalization.  For plotting purposes, I want to be able to extract the post-normalization...A",2),rep("B",2),rep("C",2),rep("D",2), rep("E",2)) pData0 = data.frame(cbind(samples, condition), row.names = samples)<span style="line-height:1.6">#<…

deseq2 r ruvseq normalization rnaseq

updated 10.4 years ago • nickp60

p/101210/ Below is an example of the code I am running and the errors I encounter: ``` library(DESeq2) countdata<-read.table("T1.txt", header=TRUE, row.names=1, check.names = F) class(countdata) countdata<-as.matrix(countdata...class(countdata) condition<-factor(c("Control,"Treatment")) (coldata<-data.frame(row.names=colnames(countdata), condition)) coldata dd…

DESeq2 DEG

updated 3.9 years ago • priya.dalvi

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 7.8 years ago • umahajan

I ran DESeq2 version 2.12.2 with the following code: <pre> Meta<-read.csv("BAT_Meta.csv",header=TRUE,row.names = 1) Raw<-read.csv...BAT_Raw.csv",header=TRUE,row.names = 1) dds<-DESeqDataSetFromMatrix(countData = Raw,colData = Meta,design = ~condition) dds$condition<-factor(dds$condition...of ?results [2] see 'independentFiltering' argument of ?results</p…

deseq2

updated 9.6 years ago • nschaum

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 7.7 years ago • twtoal

is happening? __DEseq2:__ countdata=as.matrix(read.table("2014\_04\_06\_6h\_Co2.csv",header=T, sep=",", row.names=1)) coldata= read.table ("targets.csv", header = T, sep=",",row.names=1) dds <- DESeqDataSetFromMatrix(   countData = countdata...results(ddsLRT) __sSeq:__ countdata=as.matrix(read.table("2014\_04\_06\_6h\_Co2.csv",header=T, sep=",", row.names=1)) conds.data=…

deseq2 sseq

updated 11.2 years ago • Catalina Aguilar Hurtado

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 4.9 years ago • amoaristotle

Hi everyone, Sorry for the inconvenience, I was hoping that @mikelove in particular could help me. On the same dds DESeq2 object, I performed a DGEAnalysis with DESeq2, through 2 approachs : - One all-steps-in-one ```r dds <- DESeq(dds) ``` - and one step-by-step dissected ```r dds <- estimateSizeFactors(dds) # normcnt <- counts(dds, normalized=TRUE) # write.csv(normcnt, fil…

DESeq2 Normalization

updated 21 months ago • RL

Let's say I have an RNAseq experiment of 12 samples. There are 3 subjects, 2 cell types (B and T cell) and 2 diseases (SLE and HC). I combine cell type and disease into a single combined variable called group, such that it is a factor with 4 distinct levels. Let's say that there are 15k genes detected and each sample has a library depth of around 20M uniquely mapped reads. I then go through th…

DESeq2

updated 3.3 years ago • jeffrey.maurer

Dear  [Michael Love](https://support.bioconductor.org/u/5822/): I used fpkm(dds) form DESeq2 R package to calculate fpkm , the progress did not show any error. The I summed all gene's fpkm value belong to 1 sample...Dear  [Michael Love](https://support.bioconductor.org/u/5822/): I used fpkm(dds) form DESeq2 R package to calculate fpkm , the progress did not …

deseq2 fpkm()

updated 7.6 years ago • lyrae

Hi all, In the analysis of differentially expressed genes with Deseq2 I would like to understand : 1. what is the difference between Value and Padj? 2. Would an analysis based only on Padj &lt...Hi all, In the analysis of differentially expressed genes with Deseq2 I would like to understand : 1. what is the difference between Value and Padj? 2. Would an analysis based only on Padj &am…

rnaseqGene DESeq2 Transcriptomics

updated 4.2 years ago • diangomaiga

Hi all, I would like to use DESeq2 for the analysis of a pooled shRNA screen to identify mutation specific lethals. The design of the experiment is a...Hi all, I would like to use DESeq2 for the analysis of a pooled shRNA screen to identify mutation specific lethals. The design of the experiment is a number of mutant cell lines and a number of wildtype cell lines. For every cell line there is a…

deseq deseq2

updated 10.9 years ago • c.lieftink@nki.nl

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 17.7 years ago • Wolfgang Huber

I have biological states called sample1, sample2 and negative control (NC) in duplicate. They are all from the same sequencing run. I wrote R code using DESeq2 which generates all pairwise comparisons...raw reads in a file `` expr_table.csv ``, i.e. a file with seven columns. I seems to me that when DESeq2 deals with one pairwise comparison, then the raw reads in the expression table of the sta…

deseq2

updated 8.5 years ago • anton.kratz

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 5.4 years ago • olegderyagin

I am running the DE analysis using Deseq2. When I plot the PCA of differentially expressed genes ( ntop=500) using the command below, I do not see a clear difference...ggplot(data, aes(PC1, PC2, color=treat)) + geom_point(size=3) + geom_text_repel(aes(label=row.names(data))) + xlab(paste0("PC1: ",percentVar[1],"% variance")) + ylab(paste0("PC2: ",percentVar[2],"% variance")) </pre> <im…

deseq2 pca

updated 9.7 years ago • g.atla

<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 20.4 years ago • Suresh Gopalan

Hi, I am using DESeq2 to analyze differential expressed genes (DEGs) from counts generated by Illumina sequencing. I have a 3-factor experiment...treatment:timepoint + genotype:treatment:timepoint)?. So, I tried as follows: <pre> library(DESeq2) # Load row counts countData<-read.delim("all_counts_matrix_T1_T2_T3", sep="\t", header=TRUE, row.names = 1) col_ordering...integer…

deseq2 bioconductor rnaseq multifactorial design interactions

updated 9.4 years ago • c.evang

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 2.3 years ago • question_guy

all, in relation to my mail from January this year, I followed Simon's advice to do my analyses in DESeq2 instead of DESeq. I am working on an RNASeq from c. elegans. I have mapped the data with the ensembl genome build WBcel215...replica. Now I am trying to find differentially regulated genes between the two conditions using DESeq2. This is the script I am using to read my raw count table int…

RNASeq DESeq DESeq2 RNASeq DESeq DESeq2

updated 11.5 years ago • Assa Yeroslaviz

Syed" <mosvey@gmail.com> wrote: > Thanks Michael, > I have more questions regarding my Deseq2 analysis. If I have three > conditions, ( Transcriptome at three different stages during development), > Which > way...down the gene list. In my previous email I > suggested you could filter by effect size (and in DESeq2 v1.4 you can use > the LFC t…

Transcription DESeq DESeq2 Transcription DESeq DESeq2

updated 11.7 years ago • Michael Love

Hello All, I would like to generate an HTML report from DESeq2 results of RNASeq analysis. I have followed the example in the ReportingTool documentation and have no problem with...Hello All, I would like to generate an HTML report from DESeq2 results of RNASeq analysis. I have followed the example in the ReportingTool documentation and have no problem with that, but unlike that example my dese…

reportingtools publish deseq2

updated 10.8 years ago • noushin.farnoud

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 11.7 years ago • Guest User

Hi, I am using DESeq2 with this model matrix (dput of the model matrix and DESeq2 command are pasted below). However, DESeq2 complains that...2L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0", "1"), class = "factor")), class = "data.frame", row.names = c("s1_a", "s2_a", "s3_a", "s4_a", "s5_a", "s6_a", "s1_b", "s2_b", "s3_b", "s4_b", "s5_b", "s6_b")) dds <- DESeqD…

deseq2

updated 6.8 years ago • arielle

Hi, I used DESeq2 to analyze RNA-Seq data, and obtained some results that are hard to explain. Could anyone help me? Please see the...Hi, I used DESeq2 to analyze RNA-Seq data, and obtained some results that are hard to explain. Could anyone help me? Please see the following...figure is MA plot which shows the result of differentially expressed genes identification us…

deseq2

updated 8.0 years ago • jQ

I have just upgraded my R to 3.2, bioconductor to 3.1 and then installed the latest DESeq2 package and now a DESeq analysis that used to work keeps failing with the same error. Here is what I have been doing: <pre...gt; register(MulticoreParam(12)) > countData<-read.csv("counts.csv",header=T,row.names=1) > colData<-read.csv("sample_meta_data.csv", header=T, row.n…

deseq2 error

updated 10.3 years ago • frankS

do if we have a variable considered as "Batch" and we want to use `lfcshrink`. In the vignette of [DESeq2][1] appears that the shrinkage estimator `apeglm` cannot handle contrasts but the design can be rearranged and nbinomWaldTest...package="pasilla", mustWork=TRUE) cts <- as.matrix(read.csv(pasCts,sep="\t",row.names="gene_id")) coldata <- read.csv(pasAnno, row.names=1) …

BatchEffect lfcshrink RNA-seq DESeq2

updated 2.4 years ago • Eva

PC2 + PC3: Pre/post treatment timing (regardless of medicine vs. placebo) Therefore, I designed a DESeq2 interaction model including the covariates (paired sample information, batch, sex, age). The code is shown below. However...Could you provide advice on the best way to analyze this paired treatment dataset? ```r library(DESeq2) countData <- read.csv('count.csv', row.names=1, che…

DESeq2

updated 28 days ago • Junmo

_rep1     Str\_C\_6hr\_rep2   R code I tried as of now:     library(DESeq2)     count\_table<-read.table("all\_expr.txt", header=T, row.names=1, sep="\\t")     batch<-factor(c(rep("stress..._A",6), rep("stress\_B",7), rep("stress\_C",6)     exp\_design<-data.frame…

deseq2

updated 7.1 years ago • sancharisircar24

pipermail/bioc-devel/2023-January/019398.html We face an error while running `CMD check` for DESeq2: ``` > ### ** Examples > > > # some artificial data > cts <- matrix(c(80,50,1,100, + 1,1,60,100, + 0,50,60,100), ncol=4, byrow=TRUE) > # make a DESeqDataSet...gt; dds <- DESeqDataSetFromMatrix(cts,…

DESeq2

updated 2.8 years ago • martin.grigorov

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 16.9 years ago • Boris Umylny

Hi all! I want to create a shiny app for DESeq2 analysis. My main thought is to upload count matrix, extract colnames/experiments and provide an editable table to...experiment (-> colData). After adjustment, user has to click a button in order to start DESeq2. However, when I click the button, I get following error: > Warning: Error in DESeqDataSet: the design formula contains…

deseq2 shiny design rhandsontable hot_to_r()

updated 6.8 years ago • hinkel2

Hi, I use DESeq2 in R for differential expression calculation. I already know the design is terrible, but this is what I have to work...Hi, I use DESeq2 in R for differential expression calculation. I already know the design is terrible, but this is what I have to work with ;) Question 1: can I remove the batch effect between 2 groups if their samples do not share a batch, but some of their sa…

deseq2 batch

updated 6.2 years ago • Solarion

Hi, when I got my DESeq2 analysis result, I found the log2Foldchange values are between -1 to 1. But when I checked the normalized read counts...Hi, when I got my DESeq2 analysis result, I found the log2Foldchange values are between -1 to 1. But when I checked the normalized read counts, I found they are hugely different between my two types of tissue (3 replicates for each type). Is that normal?…

DESeq2

updated 4.1 years ago • Cheryl

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 8.1 years ago • cg

tried to duplicate the DESeq2 result by explicit calculation and found the result to be drasically different from the one performed...with DESeq2. I would appreciate it if anyone could please tell me if I am using the wrong formula for the explcit calculation or...I am using DESeq2 incorrectly. ```r > library("DESeq2") > coldata=read.table("data/targets.3.txt",sep="\t",…

DESeq2

updated 4 months ago • richardallenfriedmanbrooklyn

Hi. I'm very new to coding, but am trying to run the DESeq2 package for an expression analysis and am having trouble that I think should be relatively easily dealt with. The...Hi. I'm very new to coding, but am trying to run the DESeq2 package for an expression analysis and am having trouble that I think should be relatively easily dealt with. The design...in advance for any help ``` OT…

deseq2 comparison design paired treatment

updated 6.1 years ago • tinglec

Dear all, I was wondering if I could get advice on a complicated model for DESeq2? Currently, I have different mutations in two cell lines that are tissue-relevant (neurons and glia) with multiple replicates...for each. Essentially, I have a double knockout (0), heterozygous knockout (1), wild type (2), and duplication (4) for each of these mutations (gene dosage). I am trying to make a model …

deseq2 rnaseq

updated 5.9 years ago • NeuroGeneticsBoy

I was asked to run DESeq2 on RNA-seq libraries, 2 replicas x 2 conditions (I know it is not ideal but that's how the data is). I notice that there is a...I was asked to run DESeq2 on RNA-seq libraries, 2 replicas x 2 conditions (I know it is not ideal but that's how the data is). I notice that there is a small...06 Here's how I run the analysis, just default parameters design&…

deseq2

updated 5.7 years ago • ninova

on a RNAseq dataset and found a strange problem in the result. The raw data set, the code, and the DESeq2 output were shared in a [Google Drive][1]. In the DESeq2 output, I ranked the genes by the ascending order of the column "padj...the normalized read counts of the 30 samples, calculated using counts(dds, normalized=T), to the DESeq2 statistics. When we examined the gene list, we found someth…

DESeq2

updated 5.0 years ago • Dejian Zhao

a fairly simple question that I know has been addressed many times: I want to import RSEM data into DESeq2 for modeling and DE. For reproducibility, the workflow is: Unfortunately, it is costing me an inordinate amount of time...and I cannot find a perfectly analogous example either in any vignette (for DESeq2, tximport, tximeta, tximportData, etc) or in other posts. # Load libraries libsN…

tximport tximportData DESeq2

updated 2.5 years ago • vlaufer

div class="preformatted">Dear Michael and DESeq2 users, I started using DESeq2 three weeks ago. Even I was having some normal problems for a newby person my experience...before. My RScript is: #Count matrix input Cele_MRvsER_old = read.csv (file.choose(), header=TRUE, row.names=1) CeleDesign <- data.frame( row.names = colnames(Cele_MRvsER_old), condition = factor(c("MR", "MR", "E…

DESeq2 DESeq2

updated 12.2 years ago • Alicia R. Pérez-Porro

Hi, I am doing a DESeq2 analysis using a data set of nine different conditions/time-points. I first ran the analysis with the complete data...Hi, I am doing a DESeq2 analysis using a data set of nine different conditions/time-points. I first ran the analysis with the complete data set in the count table and than have used the results function to extract the pair-wise results of the DE ana…

deseq2 differential expression independent filtering pre-filtering design matrix

updated 10.7 years ago • Assa Yeroslaviz

Hello, I am running DESeq2 from bulk RNA sequencing data. Our lab has a legacy pipeline for identifying differentially expressed genes, but...for visualizations, etc. to make it cleaner: ```r # Create coldata coldata <- data.frame( row.names = sample_names, occlusion = factor(occlusion, levels = c("0", "70", "90", "100")), region = factor(region, levels = c("upstream", "downstream.…

DESeq2

updated 6 months ago • Alexander

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 8.5 years ago • linda.c.dansereau

Dear DESeq2 developers & Bioconductor community. I was hoping somebody could clarify/confirm on how to use the following experiment...data in DESeq2: 1. I have pairwise expression data from two distinct loci, A and B (the position), and under two different conditions (treated...between condition treated vs. untreated.   The data is available in quadruplicates(untreated)/dup…

DESeq2

updated 10.5 years ago • Maurits

Hello, In addition to the Deseq2 manual, these are the posts that I read before coming up with the code. [grouping][1] [design][2] I have converted my data into...series data as follows. ```r # Reprex for the phenotype data colData <- data.frame( row.names = c("DY32156","JZ72116","ZX19451", "GC93380","ZC5448","YW112","MU27846","MP37616","LN…

TimeSeriesExperiment RNASeq design DESeq2

updated 4.1 years ago • Kesava

ve read myself into a stand-still regarding how to best optimize the different variables within the DESEq2 package for my particular data. I really want to better understand the details of how Deseq2 processed my counts My...subject_metadata_deseq2.csv", row.names=NULL, fill=TRUE) # now make this a factor as it will be the variable we will use define groups for the differential expression...1…

DESeq2 RNASeq

updated 3.3 years ago • marinawakidanna

regardless of cell line background. This is the opposite scenario from the one described in the DESeq2 documentation for the fission dataset and I am unsure how to proceed. Please help! I have three cell lines (X9342, X10742...res$padj),] resdata <- merge(as.data.frame(res), as.data.frame(counts(dds, normalized=T)), by="row.names", sort=F) write.table(resdata, file="filename.txt", sep…

deseq2

updated 6.4 years ago • jhnwphillips

I use DEseq2 to analyse the RNA-seq data out of an animal experiment (two conditions and two gender). The conditions include HS and...Cheers, Wei ``` #import count file countall<- read.table(file.choose(),header = F, row.names = 1) countall <- as.matrix(countall) #load libraries library(DESeq2) #Assign condition condition <- factor(c(rep("Control

deseq2 ~group

updated 5.6 years ago • weichengz

<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 17.2 years ago • Gordon Smyth

I want run deseq2 from tximport data. for sample dataset I can able to create deseq2 matrix file but for own data getting error i have kept...after updating the version getting same error please help Thank you ```r library(DESeq2) library(tximport) dir <- "counting" samples = read.table('Sample.txt', sep="\t", header = T, row.names = 1) tx2gene = read.table('Transcript_g…

DESeq2 tximport

updated 21 months ago • hemantcnaik