Bioconductor Forum

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 6.2 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 5.5 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 5.3 years ago • evelas13

Hi All, I am trying to collapse technical replicates in DESeq2. Already had a look at the manual, but still is not clear to me how to do it. I did try run it but got some errors, need to understand...nbsp;  5        25   24 > dds$Subject <- factor(sample(paste0("Subject",rep(1:22, c(1,1,2,…

deseq2 collapseReplicates

updated 10.5 years ago • Catalina Aguilar Hurtado

I have experienced very good results with DESeq2 for my RNASeq analysis. As far as I understand, it is a tool that normalise our data from sequencing to make them...I have experienced very good results with DESeq2 for my RNASeq analysis. As far as I understand, it is a tool that normalise our data from sequencing to make them comparable...to make a differential…

differential expression proteomics

updated 8.0 years ago • cardin.julie

<div class="preformatted">Thank you for your quick reply Simon. I am inexperienced with R and do not know how to check if all my genes contain a zero in at least one of the samples. I'm sorry for my ignorance, but if someone would explain or point me to an explanation of how I could check this, I will certainly check this. However, I have used the commercial software CLC Bio to map each sam…

Alignment DESeq2 Alignment DESeq2

updated 11.6 years ago • Caleb Bostwick

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 4.2 years ago • jac

are: 1. In the users' guide 2.5.6, it mentions that normalization takes the form of correction factors that enter into the statistical model. Such correction factors are usually computed internally by edgeR functions...but it is also possible for a user to supply them.I would like to supply the correct factor to edgeR, how could I do this? 2. I also would like to compare the testing results of …

Normalization edgeR Normalization edgeR

updated 11.9 years ago • Guest User

Hi, I am trying to build a model for DESeq2 analyses. In past I have done simpler version of analyses where the model was not so complicated. I have few questions...Hi, I am trying to build a model for DESeq2 analyses. In past I have done simpler version of analyses where the model was not so complicated. I have few questions and I will sincerely appreciate if someone from his/her experience ca…

DESeq2

updated 2.4 years ago • Abhishek Singh

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 7.7 years ago • Arying

the contrast for the interaction terms. I've used this [tutorial][1] for writing contrasts in DESeq2 for RNA seq results and thought the approach would work in DiffBind. ```r DBA <- dba.contrast(DBA, design = '~ Condition * Treatment...DBA$DESeq2 $names [1] "Intercept" "Condition_MUT_vs_CON" [3] "Treatment_A_vs_SAL" "Treatment_B_vs_SAL" [5] "Conditi…

DiffBind

updated 4.7 years ago • lindsaynhayes

I've used DESeq2 previously on my 16S microbiota data, where I ran the phyloseq_to_deseq function then went straight on to the deseq...package (V1.22.2 I think) I can no longer do this as I get the following error: estimating size factors Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, : every gene contains at least one zero, cannot

deseq2

updated 6.1 years ago • watsons2

vs. R1 Treated), but when I run DESeq with my group levels, it appears that the results from DESeq2 are already contrasting levels against a single level (P1Treated). Am I inputting the groupings wrong for my type and...dds <- DESeqDataSetFromHTSeqCount(sampleTable=a, design= ~type+condition) dds$group <- factor(paste0(dds$type, dds$condition)) design(dds) <- ~ group …

deseq2

updated 8.1 years ago • Nmabe

I am analyzing differential gene expression from an RNA-Seq experiment in which two factors were applied. I have multiple replicates among samples when just Factor 1 is considered, and there is significant...clustering among the groups. When Factor 2 is considered as well, there is one group that has no replicates of Factor 2 at a certain level of Factor 1, while the other...levels of Factor 1 ha…

rnaseq edger differential expression dispersion

updated 9.2 years ago • nancyjwahl7

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 7.0 years ago • coyoung

extensively read the manual and other forum posts but am struggling to find a solution. I am using DESeq2 to analyse my data set but running into problems with an interaction term in the model design. To break down the experiment...se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors > #try to set reference level …

RNASeqData RnaSeqSampleSize DESeq2

updated 2.1 years ago • Mimi

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 5.9 years ago • petitechiarina

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 6.1 years ago • snatanf

following error, <pre> Error in as(mcols(gr)[, i], type[i]) : no method or default for coercing "factor" to "NA"</pre> My operations shown below > library(SomaticSignatures) > data(ov_tcga, package = "SomaticCancerAlterations...gr)[, i], type[i]) : no method or default for coercing "factor" to "NA"&…

r packages somaticsignatures variantannotation

updated 9.5 years ago • solo7773

Hi, I am new to bioinformatics. I use EdgeR. I analyze a study in humans with 3 factors, each having about 5 levels. Can this pose a problem for modeling for differential analysis? Can explicatives variables

RNAseq factors

updated 2.7 years ago • Nathalie

DESeq2 offers and suggested gene-level differential expression methods. Using the tximport vignette to import transcript...estimates, __is it okay not to sum them to the gene level and use the transcript level estimates for DESeq2 standard workflow?__ This would be an additional question in the line of my previous question. I have a 2x2 factorial...tissues; flag leaf and panicle at maximum booti…

deseq2 deseqdataset transcripts

updated 8.7 years ago • tarun2

all, I have a data set of ~360 human samples, which I would to analyse for differential expression (`` DESeq2 ``) as well as differential exon usage (`` DEXSeq ``). As we have quite a complicated data set, I would like to know if it is possible...to calculate multiple factors in one design and if it make sense in general. our data has three main categories as well as multiple sub-categories...…

deseq2 dexseq multiple factor design multifactorial design

updated 9.8 years ago • Assa Yeroslaviz

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 o…

deseq2 rnaseq

updated 6.5 years ago • badribio

trying to run MAST on a subset of single cell types, but I get the following error: Error: grouping factors must have > 1 sampled level Grouping factors are: ``` group ngeneson replicate neuroblastoma.Bridge -0.791254569558456...0) colData(sca)$ngeneson <- scale(cdr2) # store the columns that we are interested in as factors label <- factor(colData(sca)$condition)…

Mast mastR MAST

updated 22 months ago • Andrew

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 9.6 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 5.9 years ago • Zohaib Anwar

Hi. I have a problem about different DEG result from analysis same data using DESeq2 and edgeR. Here is two raw all DEG result without fiter based on |logFC| and padj/FDR ``` # DESeq2 23000 gene baseMean log2FoldChange...gene. But the padj and FDR are very different! If I use |logFC|>1 & padj/FDR < 0.05,then DESeq2 will remain about 400 gene, but edgeR only leave 4 ge…

DESeq2 edgeR

updated 6.2 years ago • 15958021290

Hi there, may I ask how i can obtain the normalization factors for each sample for this **offsets and Loess** normalization? I would like to scale my bigwig file according to the normalisation...factors. However, I can't seem to find the `$norm.facs` object within `tumor_normal_normalized_loess_blacklisted`, which can...from `deepTools`. Also, should I scale my bigwig files according to their res…

DiffBind

updated 20 months ago • Henry

Hi, I'm a researcher trying to use DESeq2 for analyzing differential loop for fit-hichip results. I'm curious if I can use it like analyzing differential ChIP...seq using raw contact counts. I gave a try using DESeq2 for differential loop and the MA plot result was non-symmetric. Somebody told me it could be the effect of trended biases...So, I'm trying to correct or remove trended biase…

hichip DESeq2 fithichip differentialloop

updated 4.9 years ago • woongjaej

div class="preformatted">Dear DESeq2 users, Simon Anders, Wolfgang Huber and I have posted a preprint describing the DESeq2 methods to biorxiv: http://biorxiv.org

DESeq2 DESeq2

updated 11.9 years ago • Michael Love

Hi, I am using DESeq2 and after the rld transformation I plotted the PCA and found an interesting result. However, I don't know how to extract...variance are explained by those principal components. Please let me know if this is possible within DESeq2 or if I should use another package. Thanks

deseq2 pca

updated 10.5 years ago • tj.hu

variables, I want to preserve the information about the treatment in the sample. I have used DESeq2 to variance stabilizing transformation of the gene expression, stored in the vst\_df dataframe of the code snippet...below. I have following question: Q: I am using first and second confounding variables as batch and batch2 information in the removeBatchEffect function. The third confounding...1 …

limma removebatcheffect deseq2

updated 9.6 years ago • ompandey

I am currently working on an analysis of two factors with two replicates each. I have called peaks using three different peaks callers, and would like to first derive a...consensus of the peak callers for each factor before generating a consensus across the factors. Is there any way i can achieve this without having to create multiple...DBA with ALL samples, replicates and peak calls (2 x 2 x 3 =…

diffbind

updated 5.9 years ago • Jim

As far as I understand, The process by which DESeq2 models a batch effect is close to : Subtracting the arithmetic mean of the batches' expression values from the genes...on a per-gene basis. Is it possible in DESeq2 instead of modelling only an additive batch effect, to model a multiplicative one as well? For example, divide the expression...nicely. Later, I tried performing differential …

deseq2 batch-effects ComBat

updated 6.2 years ago • Sam

for this batch in any other way than including it in the design? I can try another tool I guess but first I would like to know if there anything else I can do in terms of visualising or controlling for this batch effect in DESeq2

deseq2 rnaseq

updated 7.3 years ago • Tash.

I'm playing around with DESeq2 and I see in the manual that the DESeq() function is a wrapper for estimateSizeFactors(), estimateDispersions() and nbinomWaldTest

deseq2

updated 10.2 years ago • Chris

have 2 control and 2 treated design <- model.matrix(~c(rep(0,2),rep(1,2))) and for Deseq2 condition <- factor(c("Control","Control","Treated","Treated"))   Now I have this questions one specifically for limma&nbsp...control , should I assign them to 0 or 1? 2- what happens after enrichment analysis (how does the Deseq2 different from limma)? …

limma

updated 7.9 years ago • Bioinformatics

I have a couple questions for a project I'm working on. First, I originally used the DESeq2 tool on a local instance of Galaxy (I find the GUI really easy to use, plus I can upload batches

DESeq2

updated 2.7 years ago • murphytho1401

I have seen peer-reviewed publications where Deseq2 is used for differential abundance analyses of 16s rRNA data. I've recently been informed that Deseq2 may not be appropriate...for analysis of 16s reads. Can anyone provide the evidence-based sources that explain why Deseq2 should not be used for microbiome data and provide any alternatives to hypothesis testing using 16s data in R? Thank

Microbiome 16s Deseq2 16srRNA

updated 3.7 years ago • Katelyn

Hello Michael, I ran DESeq2 to get DEGs between case and control groups. I know that DESeq2 filters lowly expressed genes. So is it possible to get...such as FPKM>1, to define higly expressed genes. I want to get the highly expressed genes from DESeq2 results. Thanks

DESeq2

updated 4.0 years ago • BioEpi

Yesterday I managed to install DESeq2 on my home computer but today it simply won't work on my computer at work. I install it using the following command: source...https://bioconductor.org/biocLite.R>") biocLite("DESeq2")   However, when I then use the command library(DESeq2) I get the following: <pre> > library(DESeq2) Loading required

deseq2

updated 8.5 years ago • mdroog

filtering to exclude genes with low and very high count numbers) the data range returned from a DESeq2 rlog transformation appears dependent upon the number of samples: <img alt="" src="http://i.imgur.com/6hjqjKc.png" style...http://i.imgur.com/5hCNVYR.png" style="height:288px; width:600px"/>   The VST function in DESeq2 does behave as expected (and the transformed data perform …

deseq2 rlog

updated 10.6 years ago • snsansom

Hi, I need some help analyzing my first RNAseq data. I am new to R and DESeq2 and I have been reading manuals for both. Still, I find it very difficult to figure out...nbsp;MT\_A    MT\_B    MT\_B    MT\_C    MT\_C   The first column contains the gene names.   Here is what I have so far: #Set…

rnaseq deseq2 newbie

updated 10.2 years ago • JanaM

nbsp;In almost every case, the list is of length 1, so I would simply like to extract the first element of each matrix cell list and drop all others.  Any suggestions for how best to do this?  The matrix is rather

variantannotation vcf

updated 10.7 years ago • Sean Davis

a statistical question, sorry if it's off topic. I am trying to understand the deviance returned by DESeq2. Could not find an explicit description so I assumed it would be the deviance of the fitted model compared to the saturated...mean expression. To create a reproducible example, I'll work with the pasilla data set as used in DESeq2 user guide. This code from the user guide sets up the DESeq2…

deseq2

updated 6.9 years ago • Peter Langfelder

If we look at the example of Deseq2 vignette on interaction terms: <a href="https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html...interactions">https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions</a> Table sampleName fileName genotype condition group 1 AI_s1 A1_ATCACG_counts

deseq2

updated 7.0 years ago • salamandra

high count. When running ```DESeq(dds)```, we got the following error - ``` estimating size factors Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, : every gene contains at least one zero, cannot...It is worth noting, that our data is very sparse, and most of the counts are zero. Before running DESeq2, we filtered our data slightly differently. Instead of the d…

RNASeq DESeq2

updated 2.1 years ago • Karthik

normoxia or hypoxia) plus Treatment (no drug or drug). I combined these conditions into a single factor (Group) with four levels to help with construction of the design matrix. ```r > library(tidyverse) > targets <- data.frame...Drug")) %>% unite("Group", Oxygen:Treatment, sep = ".", remove = FALSE) %>% mutate(Oxygen = factor(Oxygen, levels = c("Normoxia…

DESeq2 limma modelmatrix edgeR designmatrix

updated 4.2 years ago • rebecca.lea.johnston

Hello, Can anyone here recommend any posthoc normalisation steps following deseq2 before generating Partial Least Squared Discriminant Analysis (PLSDA) and VIP (Variance of Importance Plots)? I presume...Apologies if this seems like an uneducated question but I'm new to both 'big data' statistics and deseq2

deseq2 normalization posthoc

updated 6.9 years ago • marc.osullivan

Hi, I am using edgeR to analyze RNASeq data and I wonder about how the interactions between two factors is dealt with, especially when the normalized cpm values tend to 0 on one of the factors. I have the factors “time” (T0/T30...and “genotype” (A,B,C). In order to build my contrasts I created a dummy factor comprising all possible combinations among levels of those two factors. Please find at…

rnaseq edgeR edger main and interaction effects

updated 8.1 years ago • David Rengel

to to the number of non-zero parameters such as the Lasso. Is there something akin to this in DESeq2

deseq2

updated 8.2 years ago • kieran.mace

I am trying to analysis 40 samples htseq-count data (20 healthy and 20 diseases) with deseq2 I have read the manual of the package but I have the data ready in my workspace . It is a dataframe of 30000\*40  The first...healthy and the second 20 are the diseases  Is there anyone who can help me how to use th deseq2 for this analysis ? I know already that one can use …

deseq2

updated 7.9 years ago • Bioinformatics

like it can be done in DESeq. in the manual it says it will always regards the first factor as  the reference. But what if I want to have the second factor as a reference. Is there  a way to set this in

junctionseq relevel reference

updated 8.9 years ago • Assa Yeroslaviz

span style="font-size:13px">When install DESeq2 to iMac 10.11.6 (R 3.3.1) using the commands   <pre> > source("https://bioconductor.org/biocLite.R") > biocLite...DESeq2")</pre> I receive the following message Warning: unable to access index for repository...downloaded 14.0 MB When lo…

deseq2

updated 8.9 years ago • huzo

Hi there, I am trying to automate an RNA-seq protocol based on the normalisation function `RUVs` which determines k factors of unwanted variation in your dataset that are then fitted in the `model.matrix` that you provide to edgeR in a way like...trying to automate an RNA-seq protocol based on the normalisation function `RUVs` which determines k factors of unwanted variation in your dataset that…

RUVseq model.matrix edger

updated 5.5 years ago • lucap

them. I first modelled the count data as usual using DESeq2, after exporting in the data and study design (3 timepoints, gene of interest...countData = countdata, colData = coldata, design = ~Gene + Time) dds$group <- factor(paste0(dds$Gene, dds$Time)) design(dds) <- ~group #Run differential analysis dds <- DESeq(dds) resultsNames(dds) A_WT10vsWT0...adj values are extremely…

DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq

updated 20 months ago • james.zhang20

issue when I use zinbwave weights. So, I suspect that weights are handled differently in the main DESeq2 analysis, and in the recomputation performed when we specify contrasts as a numeric vector. However, I do not know which...on which contrast version would provide the correct results? I am using R 4.4.0 and not the newest DESeq2 version (DESeq2_1.44.0). ```r # Import libraries library(phy…

zinbwave DESeq2

updated 5 months ago • Aurélie

div class="preformatted">Hi, I have some microarrays to do analysis. It includes 2 factors: 1week old and 5week old as ageing factors (two level) , and 4_levels genotype (yw, GMH5xyw, GMH5xFOXO,GMH5x4EBP) I assume

limma limma

updated 14.2 years ago • Zhi Zhang

On running the following DESeq2 code, R crashes with the shown error message. I have tried creating the DESeqDataSet object in multiple ways and it...On running the following DESeq2 code, R crashes with the shown error message. I have tried creating the DESeqDataSet object in multiple ways and it always...that require dispersion estimates lead to R crashing and quitting. ```r library("airway") l…

DESeq2

updated 21 months ago • Shefali

population given its cell proportion.  How would you recommend to go about with this using DESeq2?  I had a suggestion to multiply the matrix by the mean of each cellular proportion and run DESeq2 on this new matrix

deseq2 rnaseq

updated 7.6 years ago • cartalop