Bioconductor Forum

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 9.3 years ago • jian_liangli

Hi I am trying to draw a PCA plot with DESeq2 but somehow I cannot use DESeq2 functions. It is a really simple code i wil be pasting below. ```r > transform <- DESeq2::rlog...unable to find an inherited method for function ‘sizeFactors’ for signature ‘"spec_tbl_df"’ > DESeq2::plotPCA(eliminated_data, + intgroup = c('WT', 'Resistant'), + returnDa…

DESeq2

updated 3.9 years ago • edusbioinfo

lt;- res.sig[order(res.sig$padj),] rld_mat <- assay(rld) cluster_rlog <-subset(rld_mat, row.names(rld_mat)%in%row.names(res.sig)) library('DEGreport') rownames(Table) <- Table[,1] meta <- as.data.frame(colData(dds_lrt

rlog transformation deseq2

updated 7.2 years ago • salamandra

Hello, I am new to DESeq2 . I have 394 unique patient RNA sequencing samples of ovarian primary tumor. After reading information about the package...the context of my data, each RNA sequencing sample represents a unique patient's primary tumor, and DESeq2 would treat these as individual replicates of the primary tumor condition, correct? Therefore, I can conduct analysis...normalization and di…

DESeq2 RNASeq

updated 24 months ago • kcarey

team, I am just getting started and learning about the basics of R. I have installed the package DESeq2 but every time I try to load the library this error shows up: > library("DESeq2") Error: package or namespace load failed...for ‘DESeq2’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources

deseq2

updated 5.8 years ago • johanna.shen

It looks like DESeq2 has been used efficaciously for MS data in published papers (<https://www.ncbi.nlm.nih.gov/pubmed/?term=26193490>). &nbsp...in which the only information is the spectral count.  For labeled MS data, it does not appear DESeq2 is being used. Thus we want to double check with you that Deseq2 is appropriate for labeled mass spectrometry counts

deseq2

updated 8.7 years ago • maduanduan8

Is there a reason that the 'per-sample' dispersion calculation was discontinued for DESeq2? I am working with ASD samples which have been observed \[ <http://dx.doi.org/10.1371/journal.pone.0016715>&nbsp...Is there a reason that the 'per-sample' dispersion calculation was discontinued for DESeq2? I am working with ASD samples which have been observed \[ <http://dx.d…

deseq2 deseq estimatedispersions

updated 9.3 years ago • bkellman

Hello, I'm processing RNA-seq data (sampleA, sampleB) with featureCounts, and DE analysis with DESeq2. In the DESeq2 output, there are only baseMean, log2FoldChange... I would like to extract the expected counts calculated...by DESeq2 (already normalized, not the raw read counts from featureCounts). Is there anyone knowing how to extract the expected

deseq2

updated 7.0 years ago • cwliu2014

Dear all, Recently, I am using DESeq2 for differential analysis of proteomics data. But I got an error: invalid class “DESeqDataSet” object: NA values are...Dear all, Recently, I am using DESeq2 for differential analysis of proteomics data. But I got an error: invalid class “DESeqDataSet” object: NA values are not...number of values. Then, the error is gone, and I got the results. I would li…

deseq2

updated 7.6 years ago • shyu

Hi, I'm a fairly new DESeq2 user and was hoping to get some help with how to correctly account for technical replicates in my dataset. Here is some example data: suppressPackageStartupMessages(library("DESeq2")) coldata <- data.frame( 'group' = factor(c(rep('group1', 4), rep('group2', 4))), 'sample' = factor(c(1, 1, 2, 2, 3, 3, 4, 4)), 'tech_re…

DESeq2

updated 2.8 years ago • sara.p

Hi, I used DESeq2 about 4 months back to analyse my data with the design: <pre> design=~species+condition+species:condition</pre> with species...condition1","condition3","condition4","conditon5")),listValues=c(1,-1/4))</pre> However, when I use DESeq2 now (yesterday) with the same design & dataset, I get different resultsNames(dds): _"Intercept", "species\_B\_vs\_A…

deseq2 resultsnames multifactorial design

updated 9.8 years ago • Ira

Hello, I used the edgeR and DESeq2 to calculate the differentially expressed genes. Of course, the results are not identical. I read many papers, and both

edger deseq2

updated 7.8 years ago • yueli7

In DESeq2 paper: _edgeR \[2,3\] moderates the dispersion estimate for each gene toward a common estimate across all genes, or toward...conditional likelihood._  However, as far as I understood the dispersion estimate in DESeq2 is also squeezed toward a common estimate but it controls for the amount of shrinkage. Is it correct? &nbsp

deseq2 edger

updated 10.1 years ago • tonja.r

Hi, Can anyone please tell me what are the main differences between Deseq and Deseq2? I guess both work on same statistical test (Negative Binomial distribution). And for my samples using DESeq package...to test for differences between the base means for two conditions. How can I do the same using DESeq2 package. I haven't found any function for this.  Thank you

Deseq deseq2 nbionormtest

updated 9.9 years ago • Biologist

Hello all: I am trying to use DESeq2 in R. I try to install the library through bioconductor, but then receive the following errors: Loading required package...Within the DESeq package. To solve the error I have uninstalled and tried install.packages(DESeq2), and BiocManager::install(DESeq2) and am still not able to download the package fully and execute my command. Is this a

deseq2 r software error

updated 6.0 years ago • lindsay

![](https://imgur.com/a/cnvCL)Dear all, Since I am using DESeq2 version 1.18.1 I observe a weird behaviour with the significant genes. As you can see on the heatmap below, the top 50 most significant genes are plotted (FDR<5%) and it is full of outliers. I am running DESeq2 with default options. I also tried to pre-filter the gene list with no success (filtering lowly expressed genes for …

deseq2 outliers version

updated 8.0 years ago • aec

Hi, I have digital raw read counts of . Whatever I am googling I am not finding anybody used DESeq2 for differenial expresseion in this assay. I have done Differential expression with DESeq2 though. In this assay the...expression levels of genes are assessed. Do you thing I can use DESeq2 for differential expression in this assay? People in this publication used DESeq2 for assay https://www.ht…

Targetedsequencing DESeq2

updated 5.1 years ago • Fereshteh

Hi everyone, For DESeq2, I am trying to understand the interpretation of with/without an interaction term in the design formula. Assume we...Hi everyone, For DESeq2, I am trying to understand the interpretation of with/without an interaction term in the design formula. Assume we have...genotypes (Mutant vs WT). Here is a simulation study and my interpretation. ``` > library("DE…

deseq2 design formula log fold change

updated 5.6 years ago • jason.taotaotan

pmc/articles/PMC4524669/pdf/pgen.1005332.pdf) in which there is this statement: "We did not perform DESeq2 analysis because estimation of the dispersion parameter with DEseq2 is unlikely to be robust with about 200 TEs, compared...the dispersion parameter using thousands of genes". How many genes is advisable to use with DESeq2? Thank you. Riccardo &nbsp

deseq2

updated 9.8 years ago • ribioinfo

Hi all. I want to ask something about DESeq2 statistics. I've got the my DESeq2 results but there are so many datas with pvalue > 0.05, so it means the differential

DESeq2 RNAseq123 rnaseq deseq2 metatranscriptomic

updated 3.2 years ago • irish.prg

Hi, I am experimenting with the use of size factors in DESeq2 (i.e. the s\_ij factors). Essentially, I would like to show that the use of gene-specific s\_ij factors, derived from external...Hi, I am experimenting with the use of size factors in DESeq2 (i.e. the s\_ij factors). Essentially, I would like to show that the use of gene-specific s\_ij factors, derived from external data, improves th…

deseq2

updated 8.8 years ago • Jonathan Cairns

I am currently using deseq2 package to normalize my data and after that I will use it to calculate p-values between my conditions. I have a question...and renormalized my data to calculate p-values. when I check some manuals I saw this: "NOTE: DESeq2 doesn’t actually use normalized counts, rather it uses the raw counts and models the normalization inside the Generalized...counts will be us…

DESeq2

updated 3.8 years ago • Elif

I love DESeq2! However, when using DESeq2 for ATAC analysis, I realized one potential issue. In the figure below: Left is a scatter plot...I love DESeq2! However, when using DESeq2 for ATAC analysis, I realized one potential issue. In the figure below: Left is a scatter plot between 2 samples (biological replicates). Each point represents the read count at an **ATAC peak**. They are…

ATACSeq DESeq2

updated 4.4 years ago • changxu.fan

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 17.4 years ago • Christine Voellenkle

Hi,   I am student in bioinformatics. I had read the nice vignette for DESeq2. There is a lot of nice information. But even if it is great, I still have a question to address and I am not sure which approach...Hi,   I am student in bioinformatics. I had read the nice vignette for DESeq2. There is a lot of nice information. But even if it is great, I still have a question to ad…

deseq2

updated 8.7 years ago • cardin.julie

Hi, I am trying to use DESeq2 package. I have some question's related to that. 1. DESeq2 manual say's in MAplot function  __Points will be colored

deseq2

updated 10.7 years ago • gv

for my data to increase detection power for differentially expressed genes. I will be using your DESeq2 package (version 1.2.5) for my filtering and differential expression analysis. Based on recommendation by a statistician...3) Adjust p-values for genes passing the filter to correct for multiple testing While the DESeq2 package was nicely written, since I am not a statistician, I am still a l…

Normalization GO Network HTSFilter DESeq2 Normalization GO Network HTSFilter DESeq2

updated 12.3 years ago • Guest User

When I try to install DESeq2 with `BiocManager::install("DESeq2")` I get an error message that indicates the package is not available for Bioconductor...version 3.17, even though the Bioconductor page for DESeq2 indicates that it is available. Any ideas

DESeq2

updated 2.6 years ago • luis.franco

I am using DESeq2 for a while now, but I never see people talking about the use of the function "estimateSizeFactors" with the option&nbsp...I am using DESeq2 for a while now, but I never see people talking about the use of the function "estimateSizeFactors" with the option  "controlGenes". For what I understand, it is supposed to be used with spike-ins, in which case DESeq2 will es…

deseq2 differential gene expression controls references

updated 7.2 years ago • cris.kgs

I had a query regarding what DESeq2 assigns as ControlGenes (housekeeping genes). As per the manual, the Normalized Counts can be determined by estimateSizeFactorsForMatrix...anyone please explain the criteria for selecting the first 200 genes as Control? Is there a way in DESeq2 which can be used to determine what are the housekeeping genes and plot their expression

normalization deseq2 sizefactors

updated 5.8 years ago • mankadeep2

skill-assessments/blob/main/RNA-Seq%20Analysis/EwS.rds libraries ```r #BiocManager::install("DESeq2") library(DESeq2) #BiocManager::install("EnsDb.Hsapiens.v86") library(EnsDb.Hsapiens.v86) #BiocManager::install("EnhancedVolcano...creat DESeq 2 object dds <- DESeq(dds) #decrease the size of the DESeq object to make DESeq2 functions faster dds <- estimateSizeFactors(dds…

KEGG clusterProfiler gsean

updated 2.9 years ago • m-bihie

I installed DESeq2 by if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DESeq2") and...it from the library I get the following error Error: package or namespace load failed for ‘DESeq2’: objects ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ are not exported by 'namespace:S4Vectors' I tried dele…

deseq2

updated 5.9 years ago • deboracasagrandepierantoni

both raw count data matrix and also TPM data of all samples. At first, We performed DE analysis on DEseq2 using the raw count data, and we got some results. Then, to make sure the signals we found is correct . We also tried to run...we found that the two analysis was not consistent. We expect that, to some extent, for signals in DEseq2 analysis, they should also have low p-values. Or maybe they s…

limma deseq2 Tutorial

updated 5.4 years ago • yuemolinn

tissue using FACS and profiled by RNA-seq, and I'd like to perform differential expression using DESeq2. I estimate that my contamination rates are generally low for my sorted cells (1-2%). Unfortunately, I believe my contamination...highly expressed genes that come out as significantly different when I analyze the counts using DESeq2 (i.e., genes I know are specific to C get some of the lowest p…

deseq2 rna-seq

updated 9.1 years ago • hughes.drew

Hi valued researchers, I may ask a question on how to extract the results of DESeq2. my design was: dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ category + gender + age + BMI...I found no up and down-regulated genes Therefore, could you please suggest as I am new to DESeq2 analysi…

deseq2

updated 5.9 years ago • Do it!

Hi, I am trying to understand the DESeq2 design formula.  I am new to RNAseq, new to DESeq2 and new to writing design formulas/matrix (not a statistician or

deseq2

updated 8.2 years ago • deeptiptl74

Hello, I performed patch-seq for 2 sets of neurons and then used DESeq2 to look for transcriptomic differences between the groups. One group consists of 7 neurons and the second group consists...my dataset. I notice that some genes which are visibly different are not picked as DE genes by DESeq2. A plausible reason for this is DESeq2 is treating the zero counts as dropouts. So, if I added a…

DESeq2 DifferentialExpression

updated 4.6 years ago • pskallurkar

span style="line-height:1.6">Hi,</span> I'm using DESeq2 for DE analysis. I followed the manual guide for DESeq2 and I was able to perform a cluster taking into account the list

deseq2 heatmap clustering file list

updated 10.4 years ago • chariko

In the DESeq2 vignette, it is stated that "Parallelizing DESeq, results, and __lfcShrink__ can be easily accomplished by loading...TRUE". In the manual, lfcShrink is also shown to have a parallel option. I am using the version DESeq2\_1.16.1 and when I try using parallel=TRUE within lfcShrink, I get: "Error in lfcShrink(parallel = TRUE) : unused argument

deseq2 lfcshrink

updated 8.4 years ago • dsull

Can anyone point me in the right direction on how to do the factorial linear modeling from DESeq2? I am just a beginner and do not have much knowledge/background in statistics.  Would you please give me a detailed...instruction or script to do the factorial linear analysis from DESeq2? Thank you so much in advance. Emily

deseq2 rnaseq differential gene expression

updated 10.8 years ago • Emily

Hi , Could someone please suggest a probable reason for the following contradiction I see with DESeq2? DESeq2 reports high logFC but the same gene expression median across condition in both normalized counts (obtained...from DESeq2) and raw counts in matrix is not difference as reported. For example, DESeq2 reports a logFC as 5 and I see literally 0 difference

deseq2

updated 5.5 years ago • Raj

redundant-one from ENSEMBL. Indeed, I remember seeing warnings during \`salmon index\` step about duplicate entries.   Thank you for improving the tutorial at the vignette. Ideally also these two which I read but failed...to understand/follow-up: <pre> <a href="https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html">https://bioconductor.org/p…

tximportdata

updated 7.7 years ago • mmokrejs

tr> <td> <p>The script that I'm using is: </p> </td> </tr> </tbody> </table> <pre> library(DESeq2) data <-read.csv("//csce.datastore.ed.ac.uk//Control1.output2.csv") se <- data countData <- as.matrix(se,row.names...Geneid", header = TRUE, sep = '\t', row.names = 1) colData <- read.csv("//csce.data…

deseq2 deseqdatasetfrommatrix rnaseq affy

updated 7.2 years ago • matthew.sinton

I am planning to use DESeq2 to compare gene expression in samples from two different species of mammals with sequenced genomes. My plan is to...I am planning to use DESeq2 to compare gene expression in samples from two different species of mammals with sequenced genomes. My plan is to use...species after they are normalized wrt library size and average transcript length as is done in DESeq2? …

normalization deseq2 across species rnaseq

updated 5.8 years ago • rmurray2050

Hello I have already installed the DEseq2 package on my R (3.6.1) however i cant load the library and I get the same error to all the different approaches i have...Hello I have already installed the DEseq2 package on my R (3.6.1) however i cant load the library and I get the same error to all the different approaches i have taken...to solve the problem. This is the error: library(DESe…

deseq2

updated 6.4 years ago • shilabr

Hello, I would like to know if the DESeq2 normalization is suitable to compare bulk RNA-seq samples with pseudo bulk single cell RNA-seq samples. In particular...of the genes without the differential expression analysis since there are no replicates. Is the DESeq2 normalization a good choice in this case? Thank you

deseq2

updated 5.7 years ago • ribioinfo

Hello, I was trying to do a DESeq2 analysis on pyrosequence data that i have, and I'm trying different software in the DE analysis. In DEseq2 my DE genes

deseq2

updated 5.4 years ago • evelas13

analysis using the Galaxy platform with the following pipeline: HISAT2 --> featureCounts --> DESeq2. Now I want to recreate the PCA plot in RStudio. In the DESeq2 manual, the command line for this is: plotPCA(object, intgroup

DESeq2

updated 4.4 years ago • jac

write.table(head(bn_group_male_padj.1_sorted,1000),"bn_group_male_padj.1.bed", quote=F, sep="\t", row.names=F, col.names=T)</pre

deseq2 deseq differential binding analysis

updated 8.1 years ago • rbronste

Hi all, I am getting some RNAseq data from my colleague and it only has the DESeq2 normalized counts. Are there any ways that I could utilize these data for downstream analysis in DESeq2?  Thanks

deseq2 normalization

updated 7.8 years ago • Arying

Hello all, I am writing to learn how to set up DESeq2 when my samples have large variation in gene counts. For example below is one row from my gene count table. <table border...of reads at gene240880, but some have zero. When I feed the whole table (with ~25k genes) to Deseq2, using pretty much default settings recommended in the DEseq2 tutorial, and looking at comparisons between condition…

deseq2

updated 7.2 years ago • Helene

I have a question regarding the use of parallel computing for DESeq2 on the server. I’ve been working with this code for the last few days & I haven’t been able to find a remedy. I have been...I have a question regarding the use of parallel computing for DESeq2 on the server. I’ve been working with this code for the last few days & I haven’t been able to find a remedy. I have been…

deseq2

updated 7.2 years ago • coyoung

Hi, I am new DESeq2 user, interested in Translation Efficiency (TE) and Log2FoldChange (L2FC) of TE. To the best of my understanding, before...DESeq2 calculates TE (RiboSeq/RNASeq), the counts are normalized with the appropriate SizeFactor. The SizeFactors take into

deseq2 normalization

updated 6.3 years ago • snatanf

I am struggling installing R package DESeq. What I am doing is : ``` source("https://bioconductor.org/biocLite.R") biocLite("DESeq2", dependencies = TRUE) ``` However, some dependencies are not available ``` ERROR: dependency ‘latticeExtra’ is not available for package ‘Hmisc’ * removing ‘/nfs/users/spoeta/R.packages/R.3.3.2/Hmisc’ * installing *source* package ‘airway’ ... ** data ** …

deseq2

updated 6.1 years ago • petitechiarina

nbsp; thank you     > count\_tab <- read.table("ASVs\_counts.txt", header=T, row.names=1, check.names=F) > tax\_tab <- as.matrix(read.table("ASVs\_taxonomy.txt", header=T, row.names=1, check.names=F, na.strings...sep="\\t")) > sample\_info\_tab <- read.table("sample\_info\_milos.txt", header=T, row.names=1, check.names=F) &…

deseq2

updated 7.2 years ago • lara

Dear Michael, i have a question regarding the usage of covariates in DESeq2 modelling. I am thinking about including a covariate, e.g. gender. 1. The model with covariate gender: <pre> condition &lt...countData = mycountdata, colData, formula(~ condition))</pre> My question: Is there a function in DESeq2 to compare if my model including gender explains (significantly) more va…

deseq2 covariates

updated 8.6 years ago • markus.schulze

I see more and more papers these days that use a read cut off before deseq2 analysis, I wonder what is the rational and/or how do they arrive at how many reads is a right number..for example from...I see more and more papers these days that use a read cut off before deseq2 analysis, I wonder what is the rational and/or how do they arrive at how many reads is a right number..for example from one..…

deseq2 rnaseq

updated 6.6 years ago • badribio

told me about the DEApp application (https://yanli.shinyapps.io/DEApp/), where they implement your DESeq2 package. However, I like to understand what is being done, so I have tried to replicate the results using DESeq2 in R in...and he told me that the code I was using seemed correct, and that maybe the problem was with DESeq2 and the new version of R (>4), where the 'results()' function d…

DESeq2

updated 4.7 years ago • Sara

v=_UVHneBUBW0) and wants to visualize the PCA scree plot to check my PCA plot that was generated in DESeq2.  Is there any way I can do it in DESeq2 or in other Bioconductor packages

pca deseq2 PCA scree plot

updated 9.7 years ago • CandiceChuDVM

Dear all, I have analyzed RNA-seq dataset, see the experimental design below. The two questions we are trying to answer are: 1. Find DE genes between different conditions. It can be seen that each condition has 4 samples (biological replicates) for which I performed pairwise differential expression using DESeq2. e.g. (A-B), (A-C), (A-D), (A-E), (B-C) .... (D-E). I can see the DE genes.…

deseq2

updated 6.0 years ago • Zohaib Anwar