2,385 results • Page 1 of 48
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…
updated 3.8 years ago • dimitrischat
DESeq2 uses GLM with negative binomial distibution to model the regressor for variance shrinkage. It is obvious that the
updated 2.8 years ago • CY
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…
updated 21 months 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 the shrinkage are a more conservative list of genes that the ones before the…
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…
updated 2.1 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
updated 17 months ago • wuyingncu
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
updated 20 months 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…
updated 11 months 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
updated 2.4 years ago • Tom
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…
updated 18 months ago • ecg1g15
Hi! How can we determine the coefficient value while applying lfcShrink() with the coefficient argument? Thanks
updated 3.1 years ago • rthapa
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…
updated 3 months ago • user230613
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…
updated 4 months 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…
updated 2.2 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 …
updated 16 months 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…
updated 4.2 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
updated 2.8 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…
updated 10 weeks 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
updated 4 months 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…
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
updated 4.3 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
updated 4.6 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…
updated 2.2 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. s…
updated 2.2 years ago • nickhir
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
updated 6 months ago • bart
If deseq2 is used to analyze the differentially expressed gene, what is the effect of outliers on the results of DEGs
updated 10 months ago • Anupama
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
updated 14 months ago • rheab1230
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
updated 5.6 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
updated 5.3 years ago • ####
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…
updated 2.8 years ago • MatthewP
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…
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…
updated 2.4 years ago • poecile.pal
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
updated 4.9 years ago • grant.hovhannisyan
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
updated 4 months ago • herny.bahus
Dear all. I am using DESeq2 for analyzing differential expression of DRIP-seq data. About [DRIP-seq][1] data, I have BAM files and BED files.(used featureCounts...I already tried DESeq2 with BAM files, but I heard that BED files can be used in DESeq2.(I am not sure it's true.) Could you tell me how to use BED files...in DESeq2 if I can use BED files for analysis? Thank you! [1]: https:…
updated 3.0 years ago • H.Chloe
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…
updated 5.4 years ago • cristian
counts by the gene length, to end up with RPK (reads per kb). Can this matrix be used as an input to DESeq2 for normalisation and differential abundance analysis? PS. No library size normalisation was done (which I intend...to do using DESeq2
updated 5.1 years ago • adityabandla
Dear all, Just a quick clarification about importing pseudocounts into the deseq2 package. I don't usually apply the bootstrapping step with the Kallisto package for deseq2 analysis. My results are...part when the tsv files are then processed by the tximport package for the downstream analysis with deseq2. Thanks
updated 9 months ago • Mozart
I want to know how to use htseq-count data for detecting DEGs by DESeq2. We can get gene expression count matrix by htseq-count, and also we can use this output in DESeq2. However, the last 4 rows...counting result. Do everyone remove last 4 rows by themselves in R ? Or are there any functions in DESeq2 to pass the raw result of htseq-count ? So, in conclusion, I want to know how to connect h…
updated 2.9 years ago • scheme4193
other R package that can do GO and/or KEGG Gene set enrichment analysis from counts generated with DESeq2? I have a set of counts generated via DESeq2, with some very nice differential expression analysis. I was thinking of...normalization, as I could then use the GOana package for GO and KEGG analysis. Can that work with DESeq2, or is there a similar package that can use counts generated in D…
updated 23 months ago • devarts
tutorial as mentioned here to perform single cell analysis: https://github.com/mikelove/zinbwave-deseq2/blob/master/zinbwave-deseq2.knit.md I could not find any documentation indicating how the weights generated by...ZINB-WAVE are actually used in DESeq2. (I am interested in the model used). Can someone explain this to me or point me to the right literature? Any help is appreciated
updated 16 months ago • prachitipprabhu
Hello. I'm trying to analyzing RNA-seq data with DESeq2 to study differencial gene expression. I have SAM and BAM files generated by samtools. How do I insert my files on R to...run DESeq2? Do I use the SAM files, BAM files or sorted BAM files? Thank you in advance
updated 8 months ago • Bioinf_Questions
about likely relationship between the `baseMean` and the `mean of normalised counts` measured in DESeq2. Thing is at the beginning of my analysis I use to filter genes with low counts dds[rowSums(counts(dds)>10) >=n despite...be a relationship between those values, I guess? Could it be that they successfully passed the shrinkage due to very high log2foldchange
updated 2.1 years ago • Mozart
I ran all my RNA Seq data through galaxy to get FPKM files from original fastq data, but I did bias correction in Cufflinks. However, the DESeq2 manual stresses that you should use raw integer counts, not normalised counts. Does cufflinks normalise the data to...to get FPKM files from original fastq data, but I did bias correction in Cufflinks. However, the DESeq2 manual stresses that you should …
updated 6.4 years ago • as9309
of these tumors within the ever and never smoker groups. In my clinical data sheet I put into DESeq2 I have 2 columns: Smoking - Y or N Type - A, B, or C I encoded this in DESeq2 as: dds <- DESeqDataSetFromMatrix(countData = cts, colData...coldata, design= ~ Type + Smoking) However, I have been asked to do DESeq2 within each subtype and compare the results across the 3. So, do DES…
updated 16 months ago • a.basitkhan1990
to do rna-seq analysis but as i ve read and been told cuffdiff is outdated and now i have been using deseq2 ( i got no idea of R but with the help of this link : https://dwheelerau.com/2014/02/17/how-to-use-deseq2-to-analyse-rnaseq-data...Results from cuffdiff also had basemeanA basemeanB ( two conditions or two samples ) but deseq2 just gives 1. Can someone tell me the code in R to add so i can …
updated 4.6 years ago • dimitrischat
I'm having difficulty performing DESeq2 analysis on FeatureCounts data from Galaxy. I've tried [both][1] [these][2] websites, but I can't seem to properly format my...I'm having difficulty performing DESeq2 analysis on FeatureCounts data from Galaxy. I've tried [both][1] [these][2] websites, but I can't seem to properly format my FeatureCounts data for DESeq2. My FeatureCounts output file from Ga…
updated 4.5 years ago • Newbieish
It's really complicated for me to handle three-factors with DESeq2, though many of the posts on Biostars.I think the developer should make it more clear to users. Three factors are temperature...5)water*co2, (6)temperature*water*co2, (7)temperature*water. I have tried a lot with design in Deseq2, like DESeqDataSetFromMatrix(countData = countData,colData = colData,design = ~co2+temperature+water…
updated 4.6 years ago • marburg2107
Hello everybody! I am trying to install DESeq2 and I keep getting errors. At first I had about 10 errors regarding packages I couldnt install. The main problem of that...From searching I managed to install RCurl but I still get the bellow error. > install('DESeq2', lib = '/home/kostas/R/x86_64-pc-linux-gnu-library/3.6') 'getOption("repos")' replaces Bioconductor standard repo…
updated 9 weeks ago • tsomakiank
I m running Deseq2 pipeline my final result file is like 18,000 genes .So how do take the differential expressed genes from my list of genes...Do i sort if based on p value or is there a way to do inside the deseq2 before getting the final list of genes Any help or suggestion would be appreciated
updated 5.1 years ago • krushnach80
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