Bioconductor Forum

Hi, I was trying to import the count result from HTSeq Count into DESeq2.  <pre> # inside of "HTSeq_Count_ChIPpeak_H3K27ac_geneX.csv" "Samplename", "countfile", "genotype", "compartment" "H3K27ac_WTCellB...in DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, : Gene IDs (first column) differ between files. In addition: Warning messages: 1: In is…

chipseq deseq2 htseqcounts

updated 7.8 years ago • JunLVI

Hi everyone, I am struggling with the implementation of the design model in DESeq2 for the following experiment: Basically I have a condition factor with three levels: Control, Asymptomatic, Symptomatic...Symptomatics - controls) - (Asymptomatics - controls)? And if yes, how would I implement that in DESeq2? I would really appreciate anyone's help! Thank you very much in advance! -Matt Edit…

deseq2 model design differential gene expression experimental design

updated 6.9 years ago • L_K

Hello Mike, Please allow me ask a basic question. What does 'log2FoldChange' in the results of DESeq2 analysis really mean for the interaction of a two-factor two-level design? Is it possible to compare 'Factor A level 1...to ' Factor A level 2' or other similar comparison? Here are the part of codes I used: dds <- phyloseq_to_deseq2(phyloseq.obj, design...Treatment*Day) colData(dds…

DESeq2 DESeq2

updated 10.6 years ago • Guest User

nbsp;design = ~Time + Treatment) dds dds$Treatment <- factor(dds$Treatment, levels=c("35", "25")) dds$Treatment <- relevel...dds$Treatment, "35") dds$Time <- factor(dds$Time) dds <- DESeq(dds) But I think th…

deseq2 rnaseq differential gene expression

updated 9.6 years ago • Catalina Aguilar Hurtado

Hi, I am running analysis on RNA Seq data using DESeq2, I have two "treatments" for each sample each with two levels status: sham or infected temperature: high or low. I have run...sham or infected in comparison to those genes sig. differentially expressed when temperature is also factored in (the interaction)? Therefore I should also run with "reduced=~temperature" to test the sa…

deseq2 Job

updated 6.6 years ago • bekah

div class="preformatted">Hello, How can I get ALL the Experimental Factors (Factor name, Factor values) from the Experiments on ArrayExpress? Thanks, -Yogesh [[alternative HTML version deleted

updated 13.8 years ago • Yogesh

Hi! Quick question about the type of count data DESeq2 expects as input: Should I avoid doing any clean-up prior to normalizing my data with DESeq2?  Currently, I remove...Hi! Quick question about the type of count data DESeq2 expects as input: Should I avoid doing any clean-up prior to normalizing my data with DESeq2?  Currently, I remove contaminant OTUs (those that were pre…

deseq2

updated 9.3 years ago • aravenscraft

in a linear model, gene expression is given by the sum of modelled variables (i.e. biological/batch factors) you have to take into account. So, in the simplest scenario: gene expression ~ factor_1 + batch Now, let's say I have the following...II ---------- **Important note**: I am using Kallisto to perform pseudoaligment and then DESeq2 via tximport (i.e. to generate a txi.kal…

deseq2 batch effect batch

updated 5.5 years ago • Mozart

KHTML, like Gecko) using:   <pre> ##DESeq2 ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("DESeq2") browseVignettes...DESeq2") source("https://bioconductor.org/biocLite.R") biocLite("data.table") </pre> From there I loaded the library backapge DESeq2...nbsp; <pre> library("DESeq2") Loading requir…

deseq2

updated 3.7 years ago • smartdogs4chris

I am trying to analyze the RNAseq data using Salmon + DEseq2. I have two variables: genotype (WT or KO) + condition ( treatment A or B), as shown below: ```r >samples # run genotype condition...I am trying to analyze the RNAseq data using Salmon + DEseq2. I have two variables: genotype (WT or KO) + condition ( treatment A or B), as shown below: ```r >sample…

DESeq2

updated 15 months ago • sykbod

I took inspiration from this sentence in chapter "3.3 Experiments with all combinations of multiple factors": "A simple, multi-purpose approach is to combine all the experimental factors into one combined factor". This approach...to build complex matrices), and specially the use of intercept term. In brief, I usually create a factor that summarizes all combinations of experimental conditions …

edger differential gene expression

updated 6.2 years ago • rfenouil

release/bioc/vignettes/GOexpress/inst/doc/GOexpress-UsersGuide.pdf I am followed the manual at first and everything works fine with the test data set (microarray data I suggest). Now I wanted to apply the package functionalities...to my RNA-Seq data that I already analyzed using DESeq2.  I think the main problem is: how to came up with a  <pre> ExpressionSet data objec…

GOexpress deseq2 expressionset

updated 9.1 years ago • martin.hoelzer

Hello, I have a question about DESeq2 count normalization in the context of 3'-end RNA sequencing. I understand that the median of rations normalization...used by DESeq2 is not suitable for within-sample comparison of gene expression, notably because it does not account for differences...1 molecule = n reads). In this context, can we do within sample comparison of gene expression of DESeq2-…

DESeq2

updated 2.0 years ago • theophile

different species. I asked this on Biostars, and was hinted by Devon Ryan to contact Bioconductor/DEseq2 with this question.  (https://www.biostars.org/p/253849/\#312451 ). Presumably, software like DEseq2 can be used to account...for such gene-level factors such as gene length (possibly also, GC %?), but it would involve advanced approaches, (offsets?). I'd be grateful for any advice..…

deseq2 normalization

updated 6.6 years ago • akozlenkov

Hello, I'm hoping to get confirmation that my line of reasoning is correct.  I'm using DESeq2 to test for log2 fold differences in microbial gene abundances across two habitats sampled using metagenomics...Hello, I'm hoping to get confirmation that my line of reasoning is correct.  I'm using DESeq2 to test for log2 fold differences in microbial gene abundances across two hab…

deseq2 normalization metagenomics

updated 9.2 years ago • jessawbryant

various antimicrobials.  I have used RUVSeq to remove a batch effect present in my data set and DESeq2 to estimate differential expression. I used the EDASeq::plotPCA function on the SeqExpressionSet generated...closer together.  I then used this SeqExpressionSet to estimate differential expression in DESeq2 with the code: dds <- DESeqDataSetFromMatri…

deseq2 ruvseq rna-seq batch effect

updated 7.0 years ago • dbouzo

I'm using DESeq2 to analyze count data from a fungal transcriptomics experiment. I've noticed that DESeq2 seems to handle contrasts...of count data oddly if all individuals belonging to the factor levels being contrasted have 0 counts. Below is some dummy code, with values taken from my data. There are two genes, eight...individuals, two individuals per condition. DESeq2 suggests that gene1 is h…

deseq2 rnaseq r

updated 9.8 years ago • tw372

My **experimental design** is as follows: 96 samples total, each of which are classified under 4 factors (in order of hierarchy): 1. Tissue (brain, pancreas) 2. Genotype (KO, WT) 3. Treatment (Control, Low, High) 4. Sex (M, F) For now, I am mainly...of syntax and logic. From what I could gather, since I established references by releveling each factor, that means if my fact…

DESeq2

updated 10 months ago • KW

Hi all! I want to create a shiny app for DESeq2 analysis. My main thought is to upload count matrix, extract colnames/experiments and provide an editable table to...experiment (-> colData). After adjustment, user has to click a button in order to start DESeq2. However, when I click the button, I get following error: > Warning: Error in DESeqDataSet: the design formula contains…

deseq2 shiny design rhandsontable hot_to_r()

updated 5.8 years ago • hinkel2

devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions Strangely, the list of differentially expressed genes is different based on...B','B') colData <- data.frame(sample = colnames(counts), group = factor(paste0(strain, "_", condition), levels=c('WT_A', 'WT_B', 'KO_A', 'KO_B')), stringsA…

deseq2

updated 4.8 years ago • germaximus

102789103 1.8569770 Sample18 Tumors 96733614 2.0323221 My first question is what is used as the reference in the default TMM method's calculation of the normalization factors? The user...of library-scale-scaled counts) is closest to the mean of 75%-iles." Presumably the normalization factor for the reference sample should be 1.0, but none of my samples have a normali…

Normalization edgeR Normalization edgeR

updated 12.4 years ago • Hoskins, Jason NIH/NCI [F]

countdata) <- htseq_count$ENSG colnames(countdata) <- metadata$Run metadata$Condition <- factor(metadata$Condition) metadata$Type <- factor(metadata$Type) library(DESeq2) dds <- DESeqDataSetFromMatrix(countData

DESeq2

updated 11 months ago • Demy

Hi Mike and community, I am recently doing DEG analysis by using Deseq2. I am trying to get differentially expressed genes in African American (AAM) and European American (EAM) prostate cancer...right way to set the level? or I have to set the level as ("EAM", "AAM")? sampledata$Race <- factor(sampledata$Race, levels=c("AAM", "EAM"))``` deseq2Data <- DESeqDataSe…

DESeq2

updated 15 months ago • Sharif

C:0mins | C:20mins | C:120mins | In essence within DESeq2, I want to get the results of C:120vsC0mins against B20minsvsB0mins. Has anyone performed this previously? If so, how...did you relevel, form new factors and specify the results? Cheers in advance

DESEq2 DESeq2

updated 17 months ago • Elizabeth

is a NSBS object that is incompatible with the current subsetting operation I then tried use DESeq2(1.4.5) and phyloseq (1.8.2) to run the same codes, it worked without any issue. I also tried the combination of DESeq2 (1.4.5...make a part of my question properly. What I really meant is to compare : >>> >>> "Factor A level 1" vs "Factor A level 2" w…

Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2

updated 10.4 years ago • Shucong Li

Hello,  I analyzed my RNAseq data with DESeq2 and currently I am trying to use it for the differential accessability estimation for ATACseq data.  However...Hello,  I analyzed my RNAseq data with DESeq2 and currently I am trying to use it for the differential accessability estimation for ATACseq data.  However, I...and Disease,  However, for ATAC s…

deseq2

updated 6.7 years ago • Lauma R

Hi! I am using DESeq2 on a RNA-seq data, and when I finally run the DESeq() function, I get a strange error, for which I am not able to get information...about anywhere. Please help. res=DESeq(result, parallel = TRUE) The first 3 lines of the result are as follows: estimating size factors estimating dispersions gene-wise dispersion estimates

DESeq2 RNASeq RNASeqData

updated 2.7 years ago • treebig44

Hi, I am very new to DESEQ2 and I am struggling to create the initial Deseq2 dataset. I have a zip file with HT-seq counts for 5 days and each has a certain...condition = sampleCondition) sampleTable$condition <- factor(sampleTable$condition) I would really appreciate any help I'm very lost with this thank you

DESeq2 timepoints

updated 3.7 years ago • Chloe

from a `` DESeqDataSet `` object that's been through the complete `` DESeq `` pipeline? At first I thought perhaps the empirical Bayes shrinkage augmented the df as it does in `` limma ``, but that doesn't appear to be the...sounds like the default behaviour of the function is to compute coefficients for each level of each factor, in addition to a model intercept. Does that mean that a …

deseq2

updated 7.8 years ago • david.watson

countsTable <- read.csv("controlvs9.csv", header=F, sep="\\t") colData = data.frame(condition = factor(c( "control", "control", "9days", "9days")))  dds <- DESeqDataSetFromMatrix(countData=countsTable, colData = colData, design...if this is ok. i was expecting to get only two: control and 9days. and also... i can't asign the first column which contains the names of t…

deseq2 bioconductor R

updated 6.3 years ago • anaQ

To build the DESeq object, I am using the ~Batch + treatment + genotype + treatment:genotype model. DESeq2 automatically converts the treatment and genotype to factor variables, but not the batch effect. So, how would it matter...if Batch was considered as a factor or as a continuous variable? 2. When I do the PCA after removing batch effect using limma's removeBatcheffect, the samples

BatchEffect batch RNASeqR formula DESeq2

updated 2.3 years ago • estafana.t98

<div class="preformatted">Hi all, I am using DESeq2 and edgeR to perform DE analysis on paired samples on a dog cancer project. Sorry if the question is redundant but I can?t find one very similar to my case. I have been designing models with 2 factors: condition (control / tumor) and patient ID (to match the paired samples). I used the model '~sample_id + condition? until now but I would…

Cancer edgeR DESeq2 Cancer edgeR DESeq2

updated 10.3 years ago • Mathieu Bahin

Hello, I've read the DESEq2 Vignette anything that Google returned from searches about "DESeq2 paired samples" and "DESeq2 Multi-factor designs...LOW > str(sampleTable) 'data.frame': 18 obs. of 6 variables: $ COL_NAME : Factor w/ 18 levels "WOP_187_CONT_S12",..: 10 13 16 1 4 7 11 14 17 2 ... $ SAMPLE : Factor w/ 18 levels "S01","S02","S03",..: 3 6 9 12 …

deseq2

updated 5.1 years ago • Benoit.Fiset

triplicate of two different genotypes (WT vs KO). It is basically the same situation as described in DESeq2's documentation in section 3.12.1.  So I have used the edgeR trick of nesting individual mice in each genotype...DataFrame with 12 rows and 3 columns grp mouse cnd <factor> <factor> <factor> D207…

DESeq2

updated 8.8 years ago • dh

Dear all, I have used DESeq2 for my Differential Expression Analysis and with ~batch + gender I controlled for the different batches. Now I would

DESeq2

updated 4.0 years ago • Bine

Dear Bioconductor Community, I am using DESeq2 to analyse a mouse RNAseq dataset and have an identical study design to one described in in example section of ?results.I...Using interaction terms dds <- makeExampleDESeqDataSet(n=100,m=18) dds$genotype <- factor(rep(rep(c("I","II","III"),each=3),2)) design(dds) <- ~ genotype + condition + genotype:condition dds &lt…

deseq2 lfcShrink interactions

updated 5.8 years ago • hannepainter

I am not sure I understand well the parameters alpha and lfc Treshold of this function : results {DESeq2} I first understood that these parameters allows to choose a p value and log fold change threshold, for example if I chose

deseq2 results

updated 6.8 years ago • Aurora

3 mutations, lets call them: mutA, mutB, mutC. I built a design matrix by putting the mutations in a factor variable along with the control. Now the variable has 4 levels (mutA, mutB, mutC, control) and I have set the "control" level...as the first level. How do I make a contrast that detects DE elements that are found in all mutated samples when compared to the control...in the design matrix si…

diffrential expression limma makeContrasts

updated 6.4 years ago • S.Bamopoulos

Dear all, I used Deseq2 to analyse differential gene expression: I have 2 factors: - phenotype (2 levels: slow and fast) - timepoint (3 levels: RT, 15...nbsp;   design= ~phenotype+ timepoint + phenotype:timepoint)  colData(dds)$timepoint <-factor(colData(dds)$timepoint, levels=c("RT", "15", "90")) colData(dds)$phenotype <-factor(colData(dds)$phenotype, levels…

deseq2 multiple factor design results

updated 8.5 years ago • koeniger

Hello, I am currently using DESeq2 to run some test on a case/control RNA-seq dataset with 2 time-point measurements (i.e. each sample has 2 measurements...nbsp;</td> <td>Phenotype</td> <td>Visit</td> <td>PatientID</td> </tr> <tr> <td> </td> <td><factor></td> <td><factor></…

deseq2

updated 7.2 years ago • o.giannakopoulou

I am working on analyzing a dataset using DESeq2. The main goal of the analysis is to compare the gene expression profiles between treated and untreated group. Since...the patients about their heart disease status. Now my question is what is the best way to write deseq2 design and contrast in order to extract something like, what are the differences between treatment groups for men...ABC1241 …

deseq2

updated 5.6 years ago • hrishi27n

might be a bit complicated post I was trying to get a better than the log2fold change to rank my Deseq2 results, so that for example to get important genes ranked poth by log2fold change and by p.value One of my colleagues...log2fold change. I do not understand the value of this and why for example not using the shrinckage factor with the sign taken from the log2foldchange, or even better the …

DESeq2

updated 17 months ago • Theo

Hi! I'm using DESeq2 on an experimental setup that assesses the effect of a treatment (control & heatwave) on 3 different genotypes (with

deseq2

updated 4.5 years ago • mep19

Hello, I am analyzing a large cohort (1000+ samples) for differential expression analysis. I am using Deseq2 to process raw counts from  samples correcting by two confounding factors (namely sex and histology origin). As output we obtain a shortlist of interesting candidates with strong adjusted p-value (e.g. p < e-14) and would like to plot the result so that I can visua…

deseq2 limma differential expression visualization

updated 6.4 years ago • Mbosio85

read.csv(pasAnno, row.names=1) coldata <- coldata[,c("condition","type")] coldata$condition <- factor(coldata$condition) coldata$type <- factor(coldata$type) ## ----showPasilla-------------------------------------------------------------- head(cts,2) coldata ## ----reorderPasila------------------------------------------------------------ rownames(coldata...cts)) …

DESeq2

updated 3.8 years ago • Anna

I have an RNA-seq counts and phenotype dataset. I have used DESeq2 to identify the differentially expressed genes, and I have also conducted Gene Ontology and Gene Set Enrichment...I have an RNA-seq counts and phenotype dataset. I have used DESeq2 to identify the differentially expressed genes, and I have also conducted Gene Ontology and Gene Set Enrichment Analysis...to get the biological functi…

TFEA.ChIP RNASeq RNASeqData

updated 2.7 years ago • treebig44

hi, i am very new to Bioconductor, and am preparing for the analysis in DESeq2 packages for RNA data. when data handling with GEO data(GSE22219), at first i got  GSE22219 data with ExpressionSet...object, so i need to convert it into DESeqDataSet class in order to use the DESeq2 package. when i handled data as below, the error message appeared. <pre> a7<-getGE…

deseq2

updated 8.8 years ago • maedakus

expression of gene B, while the second cell type is used in order to support the findings from the first cell type. I have 2 questions: First, I found some genes that had zero normalized counts in 7 out of 8 replicates (the last...a warning printed when you build the DESeqDataSet that you should > set betaPrior=FALSE because factors are present in the design with 3 or > more levels…

Regression DESeq DESeq2 Regression DESeq DESeq2

updated 10.8 years ago • Noa Henig

Hi, I have a question on how to define contrast when the design includes 2 level factors and an interaction term. design =~genome+condition+condition:genome. The resultsNames(dds): "Intercept"  &nbsp...list(c("condition\_mice\_vs\_log","genomeyb1.conditionmice")) I get the same results for the first 2 comparisons. To which of the comparisons is the contrast correct and h…

deseq2 deseq rna-seq

updated 10.0 years ago • solgakar@bi.technion.ac.il

Hi, I am using the DESeq2 (DESeq2_1.22.2) VST algorithm to normalize the tag count within peaks from CAGE-seq data. I want to use the VST transformed...I thought the VST transformed read count was the right way to go because the VST considers the size factor/dispersion to normalize the count and the unit of VST transformed read count is "count-per-million" (according to the...10-20 million VST tr…

deseq2 vst rlog

updated 5.1 years ago • juheon.maeng

contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels ``` Here is my code for the beginning (only for one time point): ``` ##Assign conditions (first four are c1, second...four are c2) conditions <- factor(c(rep("c1", 12), rep("c2", 12))) time <- factor(c(rep("0", 3), rep("3", 3),rep("5", 3),re…

deseq2

updated 4.3 years ago • DcL-A

div class="preformatted"> It is the exciting news of the coming of DESeq2. There are many updates and incorporation with other software, e.g., Wald test and cqn. My question is the nbinomWaldTest...may stuck running for long time when using multiple factors, e.g., running several days but no results or messages coming out. It works well when I remove the "type" factor. I paste the

cqn DESeq2 cqn DESeq2

updated 10.6 years ago • Guest User

Hello ! PhD student and working with rna-seq data, I used DESeq2 for my analysis but after finishing my work, I believe some elements were misunderstood when using the software. To...my work. So the design appropriated seem to be: design = formula(~G + B + G:B) Reference factors are : G1 and T1 intercept : base mean of G1 in T1 (reference) G2vsG1 : Genotype 2 against r…

deseq2 R logfoldchange rna-seq

updated 5.4 years ago • pierre.marin

1] [1]: /media/images/79219219-e1b1-4cc6-b336-2e5dabdc I also noticed that after running DESeq2, we have a higher number of differential loops on chromosomes that have cell type-specific trisomies. For example...or chr4. Overall, many of our differential loops look very convincing and I am happy with how DESeq2 is performing here. However I'm concerned that some of our differential l…

DESeq2

updated 17 months ago • Kathleen Reed

I've been using DESeq2 for differential expression analysis of microbial (meta)transcriptomic datasets and have been very happy with...I've been using DESeq2 for differential expression analysis of microbial (meta)transcriptomic datasets and have been very happy with its...in a given dataset. __My question is whether it makes sense to normalize, specifically via a DESeq2-performed size f…

deseq2 pathway analysis order normalization

updated 7.9 years ago • Matt

I have quite a few results of DESeq2 where the lfcSE is very near to 1. I don't fully understand how I should interpret this value, and though I have read through...the first several pages of google with a few different search terms, I am still not confident that I fully understand. From what

deseq2

updated 5.9 years ago • shintzen

like described in e.g. the Trinity description into one table for all samples. Striuggeling now in DeSeq2 with the function "deseqtable <- DESeqDataSetFromMatrix" we tried now the tximport package reading the manual but...54.45    0.00    17.39    0.00 without rounding it first ? Would be helpful if anyone c…

RSEM deseq2 count matrix

updated 7.8 years ago • kmeusemann

Hi, I am getting error while running DESeq2, as some of the samples contain 0 so I want to add pseudo-count to dds so that I can able to run it without any error but I...Hi, I am getting error while running DESeq2, as some of the samples contain 0 so I want to add pseudo-count to dds so that I can able to run it without any error but I am...10 dds <- dds[keep,] dds …

deseq2 r

updated 4.2 years ago • nabiyogesh

I would like to know if it is possible to use DESeq2 to analyze NimbleGene microarrays. I have a dataset of several conditions with enriched (IP) and control (Input) sample...cdc48 IP MJK503_FK2_2 561565A10_635.pair 561565A10_635 cdc48 Input MJK503_FK2_2 </pre> My first comparison would be between the IP and Input of the WT and of the cdc48 sets separately, But I would also like to try a…

deseq2 microarray nimblegene ratio limma

updated 7.2 years ago • Assa Yeroslaviz

The formula looks like this: ~ flow_cell + tissue*caste Where 'flow_cell' is a blocking factor accounting for batch effect. If i then run 'resultsNames' on the DESeq object I obtain: > resultsNames(dds_atlas_fc...contrasts within group? I am aware that a possibility is to group caste and tissue into a single factor, but we would rather keep the data structure as it i…

deseq2 interaction factors complex design

updated 5.5 years ago • c.martinezruiz