Biostar

2,961 results • Page 1 of 60

Hello all, I am trying to do an analysis for differential gene expression for rna-seq data, cell line hela for different time points. For example this is 6 to 0 hours. People told me to do the analysis with no shrinkage but i dont believe its the right way to do it for example a gene with shkrinkage is up regulated with fold change : 11...different time points. For example this is 6 to 0 hours…

RNA-Seq

updated 5.6 years ago • dimitrischat

Hi all, I have some question about the lfcshrink() function of DESeq2. When analyzed using the unshrinkage method in DESeq2, the fold change was overcalculated (Log2FC= ~30), so we are trying...to apply the shrinkage methods in DESeq2. There are three methods (apeglm, ashe, normal) introduced in the DESeq2 vignette, and among them

DESeq2 RNA-seq DEG shrinkage

updated 6 months ago • joonhong kwon

DESeq2 uses GLM with negative binomial distibution to model the regressor for variance shrinkage. It is obvious that the

RNA-SEQ DESeq

updated 4.6 years ago • CY

with countsFromAbundance = "no". A dds was created using DESeqDataSetFromTximport, then the normal DESeq2 analysis was performed. I noticed, however, an enormous amount of Differentially expressed genes: ``` out of 56570 with...2] see 'independentFiltering' argument of ?results ``` Also, when looking at the MA plots, the shrinkage using apeglm seems to shrink every non-significantly differen…

salmon shrinkage tximport DESeq2

updated 16 months ago • DCZ

I am trying to figure out which shrinkage estimater the current DESeq2 version is using in the results(..) function. The original 2014 paper describes that...Normal distribution is used as a prior, and the current vignette explains the newly avaiable shrinkage estimators (the new default is apeglm): > In DESeq2 version 1.18, we include two additional adaptive shrinkage estimators...deta…

RNA-Seq DESeq2

updated 3.5 years ago • xenia

Hi, I have been starting by first steps into RNA-Seq data and I have been performing my first analysis since two months ago. So I apologise if the question is kind of weird. I have run the DESeq2 analysis as it is detailed in the vignette and the bioconductors webpages. So far, I understand that the genes I get after...analysis since two months ago. So I apologise if the question is kind of w…

Shrinkage analysis DESeq2 enrichment differential expression GO

updated 2.5 years ago • Lautaro

Hi everyone, First time poster here - tried to look for the answer but I do not seem to find exactly what I am looking for. I have a question re log2FC shrinking as part of my DEse2 pipeline. I cannot understand which type of shrinkage I should be using. Data is from totalRNA extracted from a tissue + vs - KO of a gene of interest. Aligned to genome with STAR, deduplicated, and then ge…

DEseq2 apeglm lfcShrink

updated 13 months ago • Chiara

thing to report in results. I first decided to report the results of IHW tested results from DESeq2, from reading the vignettes this output is suggested to be a better method than the default results output by DESeq2...Is this correct? Secondly, I applied apeglm shrinkage to my dds object for plotting a MA plot, because from reading the vignettes this output is suggested to be a better...shrink…

RNA-Seq apeglm

updated 3.9 years ago • n.tear

contrast, res=dd1) Error in lfcShrink(dds, contrast = contrast, res = dd1) : type='apeglm' shrinkage only for use with 'coef' ---------- Does anybody know how to explain this? It's stuck on me for a long time

R RNA-Seq

updated 3.2 years ago • wuyingncu

Hello everyone, I apologize if this question seems a bit naive. When we ran DESeq2 for our scRNAseq data (where we first pseudobulked the data by samples), we observed that genes with low expression...Hello everyone, I apologize if this question seems a bit naive. When we ran DESeq2 for our scRNAseq data (where we first pseudobulked the data by samples), we observed that genes with low expressi…

DESeq2 DEG fold-change

updated 7 months ago • chenzy

Hi, at the moment I am analysing a simple dataset comparing two conditions using DESeq2. For DEG calling i usually go for padjust < 0,05 and foldchage of > 2. I am always wondering whether I should use for that...the shrinked fold change or the fold change deseq2 is giving me straight after the analysis. My code ist pretty straight forward using apeglm for shrinkage. A typical

RNA-Seq DESeq2

updated 3.5 years ago • ju_ra

Hi all, As I understand, s-values are calculated if using the `lfcShrink` function (with `svalue = TRUE`), instead of p-adjusted values in results. Is there a way I can get the nominal P-values (used to calculate the s- values) and also the s-values, by using the ashr shrinkage estimator? I only see the s-values. If not, which P-values is it base on? How can I examine my test by P-value histogr…

DESeq2 ashr

updated 2.8 years ago • haasroni

involved in differential expression (DE) analysis. I have read quite a few publications where the DESeq2 package is used for DE-analysis of metatranscriptome datasets. What confuses me in this context is the shrinkage estimation...of dispersion. The [DESeq2-Paper][1] reads: > In DESeq2, we assume that genes of similar average expression strength > have similar dispersion

RNA-Seq Metatranscriptomics deseq2

updated 4.2 years ago • Tom

everyone, I am trying to use Diffbind for ATAC-Seq differential data analysis. Upon comparison with DESEq2 the differential peaks are quite different. Here is my code. ```r # ------- Diffbind ------- ss <- read.csv("/mnt/beegfs6/samplesheet.csv...library = DBA_LIBSIZE_PEAKREADS) # DBA_LIBSIZE_PEAKREADS for matching results the way DESEQ2 calculate size factor using library size…

diffbind deseq2

updated 17 days ago • Ankit

I would like to plot differentially expressed genes between two specific groups (1 and 7) however as explained here http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.htmlmy "group five" is been picked alphabetically as the one to compare to. How can I select the group to which you want all the others to compare to? (Group one) resultsNames(dds) [1] "Interce…

DESEq2 RNA-Seq R

updated 3.4 years ago • ecg1g15

edgeR and DESeq2.And I wonder if someone can help me correct my understanding. 1. The edgeR and DESeq2 both use the EB method to borrow information from genes in the dataset. 2. In edgeR, the common dispersion is estimated...Then the gene-specific dispersion estimates are shrunken toward this common dispersion. 3. In DESeq2, the specific gene-wise dispersion is estimated. Subsequently, t…

estimation dipersion edgeR DESeq2

updated 7 months ago • tommy

Hello, I have just started to use DESeq2 and I am trying to compare the results obtained with and without applying lfcShrink. These are the two MA plots, one...2e3bcb54 Is it normal to lose all the significant (blue) genes with negative log2FC when applying shrinkage? I can provide the commands if necessary but are the regular ones provided in DESeq2 vignette. # EDIT: Summary of the...result…

lfcShrink deseq2

updated 2.1 years ago • user230613

Hi! How can we determine the coefficient value while applying lfcShrink() with the coefficient argument? Thanks

rna-seq

updated 4.9 years ago • rthapa

Hello, I've been diving into some journal articles about the DESeq2 model and I'm a bit puzzled about the bit on statistical testing of the log fold change. From what I gather, the log fold...Hello, I've been diving into some journal articles about the DESeq2 model and I'm a bit puzzled about the bit on statistical testing of the log fold change. From what I gather, the log fold change (after…

testing DEG DESeq2

updated 12 months ago • tommy

I'm trying to incorporate lfcShrink into my DESeq2 analysis and I'm running into a problem with the `coef` argument in lfcShrink. I performed an experiment with 4 cell lines...dds, contrast = c("condition", "cell.line.2.treated", "cell.line.2.untreated"), : type='apeglm' shrinkage only for use with 'coef

DGE DESeq2 lfcShrink

updated 16 months ago • Trivas

I'm conducting an RNA-seq gene differential analysis using DESeq2. I'm trying to shrink LFC using apeglm, ashr or even normal, but something strange is happening when plotting MA plot...I'm conducting an RNA-seq gene differential analysis using DESeq2. I'm trying to shrink LFC using apeglm, ashr or even normal, but something strange is happening when plotting MA plot, the...when using ashr. Why…

DESeq2 r

updated 2.2 years ago • loainaom

Answered by Michael Love on bioconductor** - **[Bioconductor link][1]** Hi, I am using DESeq2 v1.22.2 to test for changes in tumors over time pre and post treatment. However when I use the results function, I get...on the order of +/- 30, which is of course unreasonably large. If I follow up with lfcshrink + ashr shrinkage, these barely change and if I use lfcshrink + normal shrinkage, these e…

deseq2 ashr rna-seq

updated 4.0 years ago • Alex

set with multiple conditions (injury and treatments), and have generated many DE gene sets using the DESeq2 lfcShrink() function with the apeglm method. As the PI is preparing to publish the results he has asked that one of the...are not the same with the sign reversed, as I had expected they would be. I repeated in a vanilla DESeq2 session and confirmed that whilst the inverse comparison using …

RNA-Seq DESeq2 apeglm

updated 3.1 years ago • Chris-OHRI

Hi everyone, I have a clarification question on how the average expression versus dispersion curve is generated. From the paper, it says that Deseq2 uses 'all samples' in making the plot, but is that all samples for a given sample type (genotype) or is it all samples regardless of genotype? I am worried that gene dispersion information is being shared between genotypes, and I am wondering if t…

RNA-Seq Deseq2 dispersion gene correction

updated 6.0 years ago • brismiller

Hi, I am using DESeq2 and edgeR for my analysis. When I put cutoff of padj or FDR of 0.05 DESeq2 gives 650 DE and edgeR gives 490 DE genes But when...I apply foldchange cutoff (1) also, DESeq2 give 0 DE genes and edgeR gives 352 genes. Can anyone explain to me? thanks in advance

RNA-Seq deseq2 edger

updated 4.6 years ago • yusuf

Dear community, We are analyzing RNA-seq data from a small time-series experiment with three groups each sampled at a different timepoint (timepoint-0, timepoint-1, timepoint-2) - hence no measurements were repeated on the same individuals. The design is unbalanced with few samples in each group. To identify genes that vary over time, we encoded the time variable using two dummy variables and a…

DESeq2 RNA-Seq

updated 2.0 years ago • lams

Hi friends I have RNASeq data fromTCGA as HT-seq format. I want to do Deseq2. some patient names are duplicated and deseq2 dose not accept them. How would I deal with the duplicated patients

deseq2 RNASeq

updated 2.2 years ago • Rob

Hi everyone, I'm looking for help and guidance with interpreting my DESeq2 output since I cannot figure out what I'm seeing. I've done a bulk RNASeq experiment looking at differences between...Hi everyone, I'm looking for help and guidance with interpreting my DESeq2 output since I cannot figure out what I'm seeing. I've done a bulk RNASeq experiment looking at differences between three...t…

expression DESEq2 differential RNASeq DEG

updated 2.0 years ago • randlkc

Hello everyone, I was performing deseq2 using R and I came across the following error. I have downloaded the R scripts and deseq2 as mentioned in the biostar...anyone please help me with this issue? Also, could you please explain if this is an issue with the deseq2 or R

R deseq2

updated 6 months ago • sgadila

Hi all, My purpose of using DESeq2 is to obtain a set of differentially expressed genes for 3 different subtypes of a certain cancer and to build a classifier...using the resulting genes from DESeq2 to classify between normal and the 3 cancer subtype samples. Is there any alternate way to confirm that the resultant...of DESeq2 is appropriate for this purpose

deseq2 RNA-Seq differentially expressed genes

updated 6.1 years ago • Uday Rangaswamy

raw reads matrix for miRNAs expression and I want complete the differential expression analysis with DESeq2, how I can exclude reads with average reads below 1 (average reads of biological replicates) from count matrix before...analysis with Deseq2 ? Thanks

R rna-seq deseq2

updated 6.4 years ago • Sam

Hi I am unable to run DESeq2 **Installed** conda create -y -n test.DESeq2 python=3 conda activate test.DESeq2 conda install -y bioconductor-DESeq2...deseq2.r 3x3 > results2.csv **ERROR** Error: package or namespace load failed for 'DESeq2' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Users/xx/opt/anaconda3/envs/test.gplots/li…

RNA-Seq DESeq2 image not found

updated 4.0 years ago • ATCG

Hello everybody, I am fairly new to the RNA-seq workflow and I am currently struggling how to evaluate the performance of the RNA-seq pipeline I am trying to establish, which will be used to investigate differential gene expression. Lets say I have 3 different pipelines: 1. kallisto -> tximport -> DESeq2 -> 160 differentially expressed genes (random number) 2. …

Differential-gene-expression RNA-Seq R DESeq2

updated 17 days ago • nhaus

Hello I have two questions about DESeq2. One is about the interpretation of the output when more covariates are included in the model. Second is about the ranking...counts(dds) >= 10 ) >= 15 #Filtering for threshold dds <- dds[keep,] # Run DeSeq2 dds <- DESeq(dds, test = 'Wald') #Wald test res = results(dds, contrast = c("threshold", "TR…

DESeq GSEA

updated 12 weeks ago • noerm123

Hi, I have a question about deseq2. In the metadata of the deseq2 object I want to add a column with the ages of all included patients. However, the age of some...patients is unknown. So my question is: is it possible to run deseq2 when not all info is available in the metadata and if not: what kind of imputation technique should I use to add the missing

deseq2

updated 2.3 years ago • bart

If deseq2 is used to analyze the differentially expressed gene, what is the effect of outliers on the results of DEGs

DEGs

updated 2.6 years ago • Anupama

Hello everyone, I would like to perform a differential gene analysis on my dataset. It is composed of 8 pH points * 5 different bacterial cocultures * 3 biological triplicates = 120 samples. I have performed a de novo metatranscriptome with rnaSPAdes and now I am preparing my data to use Deseq2. I'd like to carry out two types of analysis: 1. Within my samples I have cultures of 2 bacter…

deseq2 transcriptome

updated 9 months ago • UserA

I want to do deseq2 analysis for rna-seq data. I have two replicates. I don't have any control. What should i mention in condition

featurecount DeSeq2

updated 3.0 years ago • rheab1230

Hello, I have a single question in DESeq2 usage. I have multiple groups, but each has a single sample. Therefore, I could not use DESeq2 to obtain the fold change...a plan to do GSEA, but GSEA requested a normalized data as an input. In that case, could I use DESeq2 only for normalisation? It looked ok but I want to make it sure. Thank you very much

DESeq2

updated 14 months ago • Hello

Code and warning > resLFC_sh2 <- lfcShrink(dds, contrast=c("Treatment", "Sh2", "Control"), type="ashr") using 'ashr' for LFC shrinkage. If used in published research, please cite: Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2. https...lt;- lfcShrink(dds, contrast=c("Treatment", "Sh2", "Control"), type="ashr") using 'ashr' for…

DESeq2 ashr

updated 4.6 years ago • MatthewP

Using common_precision = 196.046 as prec_init ! ! Using loess fit as a shrinkage factor ! There were 50 or more warnings (use warnings() to see the first 50) Warnings were like this: 50: In rowSums(lgamma...performed this operation with an unfiltered object. Also I am confused by `"! Using loess fit as a shrinkage factor !"`. In tutorial I saw "! Using loess fit as a sh…

RNA-Seq R sequencing software error

updated 4.2 years ago • poecile.pal

Hey All, Can one analyze affymetrix microarray data with Deseq2? I know that Deseq2 can only analyze count data but can I tweak microarray data to use it with DEseq2 (like combining perfect...values and using it). Would it be recommended considering algorithm differences between limma and deseq2

deseq microarray

updated 7.4 years ago • shashank.jatav

I want to perform RNA-Seq analysis on non-model organism data using `DESeq2` , as its well known that DESeq2 uses `Biomart` for organism references like : `hsapiens or mmusculus for human or mouse` My

deseq2 RNA-Seq

updated 7.2 years ago • ####

This may be a simple question but i don't know how to answer (I'm new in bioinformatics). Briefly, a couple of months ago I did my analysis of differential expression using DESeq2 and my last command line to obtain de differentially expressed genes between my two conditions was: results <- subset(results, padj < 0.05). After all the next data interpretation i wrote my final work and…

deseq2 cutoff differentially expressed genes log

updated 4.9 years ago • anna

Let's say I have an input for DESeq2 ready, such as: ```r library("airway") data("airway") se <- airway ``` se is an instance of class SummerizedExperiment. The object...can be given to DESeq2 directly for analysis. But how do I use it for EdgeR? The user manual of EdgeR assumes a input matrix to construct DGEList

deseq2 edgeR

updated 17 months ago • SmallChess

Hi, I'm analyzing RNA-seq data and i followed DESeq2 tutorial (http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-un-normalized

GSVA RNA-seq DESeq2

updated 2.2 years ago • herny.bahus

Dear All, For Deseq2, should I use feature counts files as input (treated vs control)? Should I include the Annotation.gff3 file as well, which

RNA-seq DESeq2

updated 8 days ago • rrehimi

of yeast, which I have obtained by mapping RNAseq reads to a diploid genome. Is it legitimate to use DESEQ2 to assess allele-specific expression for this kind of data? Thanks, Hrant

Allele-specific expression RNA-Seq DESEQ2

updated 6.7 years ago • grant.hovhannisyan

Hi, I am really confused with DESeq2. I only have normal and virus samples. I would like to see upregulated genes in virus samples dds <-DESeqDataSetFromMatrix...dds$treatment<-relevel(dds$treatment,ref="normal") Then I set the constrast after I run the deseq2 contrast1 <- c('treatment',"normal" ,"virus") I would like to get results for log2foldchange. com…

log2foldchange DESeq2

updated 13 months ago • t.ru

Dear all, I have a matrix of reads counts for each gene for each strain of an animal. I am using DESeq2 to analyse the clustering of the strains. I have performed a Variance Stabilising Transform on my DESeq2 object and...can do a PCA: p <- DESeq2::plotPCA(vsd, intgroup=c('Condition')) p <- p + labs(title = 'PCA on gene expression levels') p Now, I would like to know the coeffi…

deseq2 pca gene list loadings

updated 7.2 years ago • cristian

2,961 results • Page 1 of 60

Recent Votes

A: Blast Settings For Short Sequences

Comment: Heatmap and rna-seq

Answer: Heatmap and rna-seq

Comment: Heatmap and rna-seq

A: should FASTA files be sorted before indexed with SAMtools?

Answer: A faidx-indexed FASTA format file or a FASTA format file

Recent Locations • All