Bioconductor Forum

needing to convert my alignment output (Salmon) into a matrix file (containing raw counts) used for DESeq2. I already have my phylodb and keggannot BLAST outputs and am hoping to merge these with the counts, lengths, and abundances...that on R on the cluster since my files are too big (25G) to use on R itself, but had realized that DESeq2 does not require me to normalize my counts and only requir…

tximport Normalization DESeq2

updated 4.6 years ago • johnsony

A vs condition B after controlling for the impact of the control condition. I think I need my DESeq2 design formula to assess (Condition A- Control) vs (Condition B - Control), but I'm not sure how to reflect that in my DESeq2

designformula DESeq2

updated 2.5 years ago • Grace.Ciabattoni

Hello,   I am using DESeq2  on R (version 3.2.2) for analysis of small RNA expression data. I have some questions about how to set-up the...Hello,   I am using DESeq2  on R (version 3.2.2) for analysis of small RNA expression data. I have some questions about how to set-up the experiment...Anox\_countData\_sample,colData=colData,design = ~…

deseq2 LRT multifactor contrast interactions

updated 9.9 years ago • rclaire

I''m new to R and deseq2 so apologies I'm made silly mistakes. I have three conditions with three replicates each. They are control, infection...and attenuated infection. I have carried out analysis using 3 factor levels and used a contrast afterwards. I want to look at whats different between infection and attenuated infection

deseq2 r filtering bioconductor

updated 9.4 years ago • rattigak

the MEF expression contamination in such a way that the resulting increased variance per gene is factored into the fold change analysis. It seems it may be possible to do it within DESeq2 or using svaseq but I can't figure out

deseq2 svaseq

updated 8.4 years ago • gpalidwor

Hello A/Prof Love, Hope you are well and looking forward to CSAMA in the Italian Alps! After reading your comprehensive machine learning slides from BIOS 735 - Introduction to Statistical Computing (plus the HarvardX youtube videos with Prof Rafael Irizarry), we were hoping for one of the ML examples to use differentially expressed genes from RNA Sequencing analysis (please point in right dir…

DESeq2

updated 18 months ago • chris2.a.white

Hello all. I'm currently having issues loading DESeq2 into R version 3.6. I upgraded Bioconductor from version 3.7 to the latest version, 3.9. I am using my school's server...Hello all. I'm currently having issues loading DESeq2 into R version 3.6. I upgraded Bioconductor from version 3.7 to the latest version, 3.9. I am using my school's server to...conduct RNA-Seq analysis. **Here …

deseq2

updated 6.7 years ago • biancaineshoch

Hi, I have been trying to install DESeq2 v1.35.0 to replicate some data I generated some time ago, but I cannot find this subversion. BioCv15 has the v1.36, whereas

DESeq2

updated 20 months ago • Espresso

Dear all, I need to describe in more detail how the built-in transformation of data of the DESeq2 function normalises raw counts. Can anyone give me a reference to a paper where this has been described? I have not been

DESeq2

updated 4.9 years ago • Bine

Hey, with the method ""plotDispEsts" of the DESeq2 package one gets a two-dimensinal dispersion plot. Here I have the following question: Can somebody explain or does

deseq2

updated 9.9 years ago • voyager.85

Dear all, I am new to RNA-seq analysis with bioconductor. I am wondering if I can use DESeq2 directly to perform survival analysis (e.g. Cox regression)? If not directly, do I understand correctly that we should

deseq2 survival rlog transformation

updated 8.1 years ago • array chip

Hi, I want to use deseq2 for RNAseq analysis. I have excel file of RNA count data with one column is geneid and others are different patients

deseq2

updated 5.3 years ago • shinemuty

shows two ways to import results for differential expression analysis at the gene level. The first approach (used with DESeq and edgeR) is to use the estimated counts from your quantification tool of choice, and let (or...which is then suitable for use by voom (presumably these can also be used (but sub optimal) in the DESeq2 and edgeR world (right?)). I'm curious about what version of the impo…

tximport edgeR DESeq2

updated 9.5 years ago • Steve Lianoglou

I used DESeq2 and found it report more deferentially expressed genes than before. Actually, it is not reasonable. I noticed the `` padj...pvalue column). I would like you to tell me the incorrect of my calculation, or some bugs in DESeq2. Thanks a lot. In the following, I pasted my sessionInfo()   <pre> > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64

Bugs deseq2

updated 11.3 years ago • lmf.bill@gmail.com

Dear all, I have been using DESeq2 for RNA sequencing-based gene expression analysis, and recently trying to use ARACNe for regulatory network inference

deseq2

updated 6.4 years ago • Tom

scaled" by dividing by the row_standard deviation. From what I have understood in forums related to DESeq2, it's because the vst (or rlog) transformations are affecting the variance of the data (since they have been designed...by the row_standard_deviation anymore. Is that right ? I am asking that because of two things: _ First, in some forums (example [here][3]), sometimes people claims that yo…

DESeq2 heatmaps

updated 17 months ago • jeba95

severity (continuous integer values). In order to be able to incorporate both my fixed and random factors (as a blocking factor), I used limma/voom <code>design <- model.matrix(~1+ targets$disease + targets$gender + targets$severity...or ribosomal proteins. These results do not make sense biologically. As a comparison, I have used DESeq2 to analyze the same data. Correcting for se…

limma voom rnaseq

updated 9.2 years ago • blofeld

I am working with the raw count data, and the metadata consists of three groups, H1, H3, and H5. Each group has four-time points, 3h, 6h, 12h, and 18h, and two treatment and control conditions. What I want is quite simple; I want to measure each control vs. each treatment at each time point in each group. No testing across time points or groups. For example, In H1 for 3h, there are two replicates…

DESeq2 edgeR R rnaseqGene

updated 2.7 years ago • DHARMESH

Hi, I’m performing a DEG analysis with RNA-seq data using `salmon` + `DESeq2`. The data were obtained from different parts of cerebral tissue and I am expecting to get a few differentially expressed...in my contrasts, because our case/control samples are quite similar (in a PCA). As described in `DESeq2` vignette, I’ve summarized transcripts estimated counts into gene counts, following `tximport`…

deseq2 edgeR salmon tximport

updated 5.6 years ago • iaradsouza1

diagnostic test for outliers called Cook’s distance caused DESeq2 (version 1.10 vs 1.30) have big different result? anyone find similar issue

version1.30 version1.10 deseq2 DESeq2

updated 4.3 years ago • Shicheng

designs with interactions_. Is there a way to get shrinked LFC values for designs with interactions? DESeq2\_1.19.14 Thanks, YK

deseq2 lfcshrink

updated 8.0 years ago • yk.gatc

Hi there, I noticed that the lfcshrink() function in DESeq2 doesn't seem to work with more complex contrast designs, eg: those with interaction terms. Is it possible for this to...Hi there, I noticed that the lfcshrink() function in DESeq2 doesn't seem to work with more complex contrast designs, eg: those with interaction terms. Is it possible for this to be

deseq2 lfcshrink interaction term

updated 7.6 years ago • krutherford

The final step of DESeq2 dispersion estimation takes a very long time to run on a dataset with 27 groups . I was wondering if there is a good strategy

rnaseq deseq2

updated 10.1 years ago • mchikina

reproducibility argument hold (between two experiments) or should one disable log2FC shrinkage in DESeq2? Thanks in advance.   &nbsp

deseq2

updated 8.7 years ago • m.f.g

preformatted">Dear Michael Love and list members, I'm used to analyze RNA-seq data with your nice DESeq2 package (1.2.0) and I sometimes have to test complex null hypotheses using contrasts. For one of my project, I would like...in results(), but it only accepts a numeric vector. Hence, I was wondering if you planned to extend DESeq2 to the use of multiple contrasts? Best regards, Hugo --…

DESeq2 DESeq2

updated 12.0 years ago • Hugo Varet

Hi All, I have received read counts per gene (48K genes) per sample after RNASeq data processing. Now I need to create heatmaps for these samples. Here is what I did: I had two types of stem cells (iPSC and ES cell) which were differentiated to three lineages in parallel (iPSC-0, iPSC-1, iPSC-2; ES-0, ES-1 and ES-2). I have 2 questions: 1. I want to analyze the read counts by DESeq2 but to my k…

deseq2 normalization

updated 5.7 years ago • Hamidreza Hashemi

I was wondering how one can do a deseq2 analysis of multiple time points when trying to test for a WT vs TREAT difference at any of the given times. Let's say...I was wondering how one can do a deseq2 analysis of multiple time points when trying to test for a WT vs TREAT difference at any of the given times. Let's say I...or to compare changes in all TP. I'm interested to understand how th…

deseq2 time-series design matrix edger

updated 6.9 years ago • Assa Yeroslaviz

Hi there, I've run DESeq2 on an RNA-seq data sets, with the count data came from HTSeq count. The DESeq() call was all by default. &nbsp...why were they not filtered out by the cook's distance or independent filtering? versions:  DESeq2\_1.18.1, R\_3.4.2. Any explanation will be greatly appreciated

rnaseq deseq2

updated 8.1 years ago • wbliu

Hello, I am working on RNA-Seq data which consists of 10 samples. My model has two factor: Time and Genotype, having 3 time point: Tbase, T45, Tend and 2 genotypes: WT, mutant (for Tend and Tbase each genotype has...Hello, I am working on RNA-Seq data which consists of 10 samples. My model has two factor: Time and Genotype, having 3 time point: Tbase, T45, Tend and 2 genotypes: WT, mutant (for …

deseq2 LRT RNA-Seq

updated 10.8 years ago • solgakar@bi.technion.ac.il

Hello, I'm running DESeq2 in combination with phyloseq to analyze 16S rRNA data coming from a large survey. I have gut microbiome coming from...to different diets) My design matrix is pretty huge so I'll not post it here but these are the first steps that I ran to get my DESeq2 object: <pre> dds <- phyloseq_to_deseq2(mars, design = ~ food + subject_id + food:subject_id

deseq2 multiple factor design interaction term

updated 7.8 years ago • Giovanni Bacci

div class="preformatted">Hi All, I am pretty new to edgeR, this is the first time I use the package, as well as the first time I try to find differential expression using RNA-Seq data (this is the first...genes between the two conditions I have a matrix of counts in tab delimited format, in which the first column is the GeneID and the first row is a header detailing the samples this is my cod…

edgeR edgeR

updated 13.4 years ago • Lucia Peixoto

three omics layers, methylation, rna, and protein) and a shared continuous time covariate. Two factors clearly capture time - both decrease over time across all groups (bioreactors = biological replicates) (and I also annotated...the factors with the help of a linear model and the meta data, and both are significant for the time meta info). When I run GSEA on the...factor loadings, the same GO t…

MOFA2

updated 7 weeks ago • Thomas

Hello, I am running DESeq2\_1.10.1 on a data set with a continuous predictor term (either with or without a categorical blocking term).   My...Hello, I am running DESeq2\_1.10.1 on a data set with a continuous predictor term (either with or without a categorical blocking term).   My understanding...inspection of Cook's distances.  I base this on section 3.6 of the N…

deseq2 outliers RNAseq differential gene expression

updated 8.8 years ago • cajawe

Hello, Can someone help me to understand the dispersion calculation of DESeq2? I don't understand what does DESeq2 : 1) If we consider two conditions A and B with n samples in each conditions, are the informations...blue on the dispersion plot but it dispersion wil be shrunked by MAP procedure). 2) Or does DESeq2 calculates the mean normalized counts for cond. A (µA) and cond. B …

DESeq2 dispersion

updated 6.9 years ago • eva-m.petit

mode > diagdds = DESeq(diagdds, test="Wald", fitType="parametric") estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates

deseq2

updated 6.6 years ago • nabiyogesh

is - should the problematic samples be excluded only or the entire subject data to be removed in DESeq2 analysis? Thanks. Regards Guan

deseq2

updated 6.9 years ago • g.wang2

nbsp;  TISSUE       REP<br/>             <factor>  <factor> <factor> <factor>  <factor> <factor> <integer><br/> A1H_Acute  A1H_Acute...SEX individual  &…

deseq2 pheatmap average

updated 7.3 years ago • chighfi

DESeq2 I installed from latest Bionconductor version is still 1.20 version. Actually, the latest version of DESeq2 is >1.4...Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0   (2018-04-23).   > packageVersion("DESeq2") \[1\] ‘1.20.0’   > sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86\_64-apple-darwin15.6.0 (64-bit) Running under: …

deseq2 R bioconductor

updated 7.4 years ago • lxl623

to be present in 'resultsNames(object)' The above syntax worked fine in my previous version of DESeq2.  Even if I try it as a list: > res <- results(dds.ps, contrast = list(c("Group", "D14", "D21") )) Error in checkContrast(contrast...of things suggested elsewhere: setting betaPrior = TRUE resulted in the following: estimating size factors estimating dispersions …

deseq2 phyloseq

updated 7.3 years ago • eoin

release/bioc/vignettes/VanillaICE/inst/doc/crlmmDownstream.pdf) And I got stuck basically at the first 5 lines! It is not obvious to me what I should do about this error. Any suggestion is appreciated.  Thanks!! Below is the

SNP6 crlmm vanillaice vanillaice crlmm cnv

updated 10.6 years ago • cafelumiere12

Hi,  Does anyone have experience with standard rna-seq analysis tools (edgeR, DESeq2, etc) to detect allele-specific expression? I have a count table in which each F1 hybrid (3 biological replicates) has...Hi,  Does anyone have experience with standard rna-seq analysis tools (edgeR, DESeq2, etc) to detect allele-specific expression? I have a count table in which each F1 hybrid…

edgeR deseq2 ase allele

updated 10.2 years ago • trianglescout

Hi, due to a strange error in DESeq my group is finally being forced to switch to DESeq2 (probably a good thing). There is one problem we are not sure how to solve, though: In the old DESeq, we would normalise the...nor with nbinomWaldTest(). Is it in this case recommended to reduce the data set before using DESeq2, for each comparison, or should we try to run the DESeq() function once and the…

deseq2 deseq

updated 8.6 years ago • LilithElina

talking about the standard normalization methods of RNA-seq data as implemented in limma, edgeR or DeSeq2 : is there any modification we shall do in the normalization method when analyzing the RNA-seq data of these 3 sets of

limma deseq2 voom edgeR

updated 6.5 years ago • Bogdan

everyone, just a quick question I am about to generate my volcano plots for DEG analysis after DESeq2. I am wondering if I should use my normal DESeq2 results, or the results I have applied LFC Shrinkage too? What is the reasoning

DESeq2

updated 3.7 years ago • axe880

data sets with triplicates. I was analyzing both the differences in each pair of time-points using DESeq2 as well as the time-series analysis using Mfuzz. I have tried to compare the expression values (or more precise profiles...created by Mfuzz and DESeq2 and got confusing results. Below is an example for one gene, its raw values as well as the calculated values from Mfuzz...and normalised valu…

deseq2 mfuzz differential expression timecourse

updated 9.2 years ago • Assa Yeroslaviz

I am having difficulty installing DESeq2 to my mac laptop. This is what it shows on my screen. When I type in library(DESeq2), it also gives me this warning. Please help...1: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'DESeq2' 2: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘tibble’…

DESeq2

updated 3.7 years ago • Jae Woong

transcript count, using salmon (with all the bias correction options activated), tximport and deseq2 : # Importing the output of salmon dir <- "./count_data_salmon" list_id=as.factor(list.files(dir)) files <- file.path(dir...tximport) txi=tximport(files, type = "salmon", txOut=TRUE, readLength=150) ##Using DESeq2 for normalisation only libr…

deseq2 salmon tximport normalization

updated 6.8 years ago • Alex So

Dear all, I would like to have some advice regarding the inclusion of certain covariates and factors in my design matrix from a human transcriptomics project. To give some more context we are comparing two different...Dear all, I would like to have some advice regarding the inclusion of certain covariates and factors in my design matrix from a human transcriptomics project. To give some mor…

RNAseq Design Matrix

updated 4.1 years ago • Barista

you tell me if there is an easy way to estimate non-trivial contrasts in MAST? E.g. there are two factors, A and B, with 3 and 5 levels, the model is Y = A + B + A*B, and I want to test (A1, B2) vs (A2, B5). I assume the answer is no because a similar...question][1] was asked of DESeq2 a while ago and MAST doesn't look different in that sense. [1]: https://support.bioconductor.org/p/81151…

mast

updated 6.8 years ago • Nik Tuzov

Hi, The following is my deseq2 design and my commands <pre> dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,directory = directory,design...Hi, The following is my deseq2 design and my commands <pre> dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,directory = directory,design= ~Sex+V11+V12+V13+V14+V15+V16+V17+Visit,ignoreRank=FALSE) dds &…

deseq2 differential expression results

updated 8.2 years ago • yoursbassanio

Hi all, I'm interested in calculating cell size factors for scRNA-seq data. The standard calculation for size factors (e.g. https://genomebiology.biomedcentral.com/articles

scrnaseq rnaseq normalization DESeq2

updated 8.4 years ago • gquon

Dear experts! The design formula of DESeq2 has been extensively discussed, however, I could not translate any example/explanation to my specific situation...Dear experts! The design formula of DESeq2 has been extensively discussed, however, I could not translate any example/explanation to my specific situation. I have two different transcriptomic experiments and I want to DESeq2 them to…

deseq2

updated 5.2 years ago • Sedlin

53 0 53 246 0 ``` Interestingly, if I run my analyse the data the way the **DESeq2** [vignette ](https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html)recommends it (+ additional...6 keep <- rowSums(counts(dds) >= 10) >= smallestGroupSize dds <- dds[keep,] ``` *#Run DESeq2* ``` dds <- DESeq(dds) ``` *#extract …

limma DESeq2

updated 2.1 years ago • michael.eigenschink

Hello, I am analyzing RNA-seq raw counts data from 5 conditions (vehicle, tx1, tx2, tx3, tx4). When I label the groups "A", "B", "C", "D", "E" and run DESeq2 on all 5 groups at once, I get a list of 7000+ differentially expressed genes (padj < 0.05). However, when I label the groups with their actual names ("vehicle", "name1", "name2", etc), my results are now ~3000 differentially express…

deseq2 multiple groups

updated 7.9 years ago • blobbyscience

B + condition) and I contrast on the level of condition. Contrast can only distinguish between two factors (e.g WT v KO, single-read v paired-end). What if my covariate "B" has four factors (a,b,c,d). So if I call dds <- DESeqDataSetFromMatrix...colData = colData, design = ~ A + B + condition) Does DESeq and results take into account the four factors of B? Or is this overlooked? If th…

deseq2 multiple factor design multifactorial design

updated 9.4 years ago • sumneuron

replicates from paired normal/tumour samples, different tumours, etc. We've had success using DESeq2 and SAMSeq on raw count data, and the high sample number has been giving low FDRs/q values. We're only interested in a small...I was wondering, then, what are the statistical pitfalls of excluding other genes _before_ input to DESeq2, SAMSeq etc? I'm aware that these apply normalisation whic…

deseq2 SAMseq differential expression

updated 9.8 years ago • aylj

preformatted"> Dear Community, I have some questions about how the DESeq r package works for multi- factors expersiment. My experiment has three factors: A/B/C, and 8 replicates per condition. I would like the test the significance...of the main effects of factor A, B and C, the significance of the two-way interaction terms: A:B, A:C and B:C, and the significance of the three-way interaction

DESeq DESeq

updated 12.0 years ago • Guest User

paired data, I am comparing the lung microbiome with the mouth microbiome in 33 patients I used deseq2 just fine with this, however when I did it in 8 patients comparing the lung microbiome over two time points (again paired...gt; otumergeinter > source("https://bioconductor.org/biocLite.R") > biocLite("DESeq2") > library("DESeq2") > datainter=phyloseq\_to\_deseq2(…

deseq

updated 9.6 years ago • l.weissenburgermoser

I have problems installing DESeq2 using R4.0.4. It tells me that it is not available for my version of R. Does anyone have an idea how to fix this? ```r > BiocManager...install("DESeq2") Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.4 (2021-02-15) Installing package(s) 'DESeq2' trying URL 'https://bioconductor.org...Content type 'application/zip' length 2863628 bytes …

DESeq2

updated 4.8 years ago • reneclassens92

genes on the X and Y chromosomes from my human RNA-seq data before doing differential analysis using DESeq2. I've looked through the _RNA-seq Workflow_ and _DESeq2_ manuals but didn't see this as an option. Any help in performing...this step and still using the DESeq2 or RNA-seq Workflow pipeline would be much appreciated. Thanks

deseq2 rnaseq

updated 7.5 years ago • anpham