Bioconductor Forum

I have RNAseq read counts for three groups of sample, each with 3 replicates. I want to find the DE genes between Group 1 and Group 2, Group 2 and Group 3, and Group 1 and Group 3. Should I combine...I have RNAseq read counts for three groups of sample, each with 3 replicates. I want to find the DE genes between Group 1 and Group 2, Group 2 and Group 3, and Group 1 and Group 3. Should I combine a…

rnaseq ruv differential gene expression R

updated 8.5 years ago • manish20072013

<div class="preformatted">Hi All, What are the different ways of detecting bad cDNA or oligo arrays using bioconductor packages? Also, what are some of the quality measures of replicates arrays (other than standard deviations)? Basically, we are always looking at many arrays (>20) simultaneously. I...bad cDNA or oligo arrays using bioconductor packages? Also, what are some of the q…

oligo oligo

updated 21.8 years ago • Anna Cao

If I try to replicate the vignette of openCyto, I get following error with automatic gating: <pre> gating(gt_tcell, gs) error in UseMethod

openCyto gating

updated 11.3 years ago • thomas.mohr

and the reduced design was ~Dx + Age + otherConfounders(sex,race…). What is the correct way to replicate the LRT analysis on the microarray data using the limma package? I am unable to figure out the appropriate commands

limma

updated 7.6 years ago • ssabunc1

<div class="preformatted">Hello ! To get the intensities of R and G channel I use RG.MA() on normalized data set. I can calculate the standard deviation using simple function sd( ). But there the spot duplicates are not taken into account, only slide replicates. After running lmFit(), eBayes() and topTable() the duplicates are accounted. But how can I get from that results the standard...…

updated 20.9 years ago • Sebastian Thieme

dataset where each gene has expression values over some time-points and each time-point has some replicates. Now how can we detect up-regulated genes between two time points using some standard procedure (may be some statistical

updated 14.3 years ago • ANIRBAN BHAR

No residual degrees of freedom in linear model fits. It is may be because I don't have replicates. So what should I do to for differential expression now. Thank you Nitin Mandloi Sandor Proteomics Pvt. Ltd., hyderabad

Proteomics limma Proteomics limma

updated 12.9 years ago • nitin mandloi

U), each at different time points. I was wondering how to design an experiment having the U replicates just at time point 0 and T replicated samples at different time-points. Is it possible to perform it with DESeq2

rnaseq deseq2 time-course

updated 8.4 years ago • inzirio

<div class="preformatted">Hello, I am new to bioconductor and I have a question about fitting and normalizing the spike-in hybridization controls. >From what I have read so far, it seems that intensity and concentration can be related by way of a langmuir isotherm. The concentrations of the hybridization controls for Affymetrix GeneChips is a known quantity. Does anyone here fit t…

updated 13.2 years ago • Matthew Thornton

<div class="preformatted">Hi, Is there a way to use DiffBind to analyse time course data? I have sample and control replicates at five different time points and I would like to know which sites show differential binding over time. At the moment...Hi, Is there a way to use DiffBind to analyse time course data? I have sample and control replicates at five different time points and I would …

DiffBind

updated 11.3 years ago • enricoferrero

Hi everyone, I have a small ChIP\_Seq dataset with 6 samples (3  replicates each of WildType and Knockout). I wanted to do a differential binding analysis with ChipComp package. When i tried

ChIPSeq ChIPComp makeCountSet

updated 9.9 years ago • AB

Is it possible to run diffbind with my "own" binding affinity table? I might want to delete certain peaks or have my own way of combining peaks across replicates. Let's say I have a table `mytable.tsv` that looks like this: sample1 sample2 sample3 peak1 312 366 12 peak2 999 12 512...affinity table? I might want to delete ce…

diffbind R

updated 5.4 years ago • maartenvandersande

linear modeling experiment. I have 3 timepoints and 4 genotypes, 2 or 4 biological replicates for each sample. Can anyone point me in the right direction on how to do the factorial linear modeling

deseq2 rnaseq differential gene expression

updated 10.7 years ago • Emily

gene expression of my samples. My example meta data is below. All samples except for sample21 have replicates; sample21 is a single transcriptome that I'm interested in looking at the gene expression for, in addition to simple...vignette('DESeq2') ``` In the meta table, I replaced the info with "TEST" to simulate replicates, and even just one worked fine with the group parameter. But...ther…

DESeq2

updated 3.7 years ago • nute11a

I used limma to analyse this and got a list of genes differentially regulated - great! THEN another replicate experiment was performed (so now I have 6 arrays, 3 dye-swaps), and I re-did the analysis and my set of genes was completely...into account biological variation, surely we can't realistically expect consistent ratios across all replicate experiments?? Isn't limma being a little harsh h…

limma limma

updated 21.4 years ago • michael watson IAH-C

Dear Bioconductor community, I have timecourse RNA-seq data. Animals received 4 differents treatments (group = GpA, GpB, GpCD, GpE). There are 6 animals in each group. For each animal,blood were collacted before any treatment (D0) and at 3 time points after treatment: D3, D7 and D28. So, the experiment could be described as follows : <pre> Animal Time Group Rep M657 …

limma-voom design matrix limma time-course limma design matrix limma

updated 7.8 years ago • SPbeginner

<div class="preformatted">Hi! I am looking for advice on how to get lists of differentially expressed genes for my experiments. Generally I have four plant lines (wt and 3 mutant lines) and two different conditions. But I do not have one common reference. I always compared treated plants to untreated pool of the same line and additonally I compared untrated mutants to wt pool. I performed 4…

Normalization Normalization

updated 17.1 years ago • Agnieszka Zmienko

td>- drug</td> <td>nd.cm</td> <td>nd.ncm</td> </tr> </tbody> </table> There are three biological replicates of each of the four conditions.  Two of those replicates were sequenced at a different time than the other replicate

edgeR design matrix contrast

updated 7.1 years ago • sdalin

supposed to include 11 timepoints for an ecotype and 12 timepoints for the other ecotype with 3 replicates each, adding up to 69 samples. The timepoints represent the annual cycle basically. However, 22 samples were lost...been informed by the person responsible for the analysis published in a paper. This leaves out some replicates out for certain timepoints while resulting in the loss of two tim…

limma RNASeq

updated 3.1 years ago • ToReality

reproducible technical discrepancy resulting from two different hybridisations. Two biological replicates for Hyb A used expired arrays, and has significantly lower intensities than the two biological replicates of...hyb B, which behave normally. I thus have 4 biological replicates of three different tissues which cluster (K-means) more strongly by hyb. than by tissue. RMA does a courageous job.…

affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma

updated 19.3 years ago • k. brand

to be a baseline measurement for both the sham and injury conditions. There are 3 biological replicates for each condition x time and each replicate is N = 20 animals. <table border="1" cellpadding="1" cellspacing="1" style="width...sham and injury conditions I decided to duplicate the control data in the count matrix (3 biological replicates of control time 0 -> 2  x…

deseq2 timecourse multiple factor design RNAseq analysis differential gene expression

updated 8.3 years ago • c.nicole

<div class="preformatted">Hello, I'm trying to analyze some toxicology data, and I got some problems with lm and rlm for which I'm looking for help. The experiment is a 3 factor design: - the value (the y vector) is a response for a treatment with a drug - a dose factor with 5 levles (a drug in 5 concentrations) - a time factor with 2 levels (time of treatment) - a batch factor with 3 lev…

DOSE DOSE

updated 21.8 years ago • Arne.Muller@aventis.com

I have a large list of genes for my plant species along with various tissue samples and multiple replicates. I used DESeq2 to obtain differentially expressed genes by conditioning the formula on the tissue type. I now...I have a large list of genes for my plant species along with various tissue samples and multiple replicates. I used DESeq2 to obtain differentially expressed genes by conditioning…

DESeq2

updated 2.1 years ago • pl23

different gene sets, coding and non-coding genes, and count data from two different conditions (four replicates of both). I want to compare how the samples cluster in the two gene sets, i.e. do they have the same expression signatures

pca deseq2 rnaseq

updated 10.3 years ago • Jon Bråte

use EBseq-HMM to analyze some time course data. In my case I have 12 time points with 3 biological replicates, 36 samples in total. When I run the pipeline, it seems that it needs an lot of resources, running it in a cluster asking

ebseq-hmm

updated 9.9 years ago • liamarseg

compare the expression 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

1 out of N samples with extreme counts. Michael Love suggested a way to force DESeq2 to look at all replicates. I've been searching for the post for a while using both Google and the forum search but I can't find it. Can somebody

deseq2 outliers

updated 8.0 years ago • paul.alto

<div class="preformatted">Dear All, The data set has 3 controls, and 9 treatments (transgenic biological replicates with different levels of gene expression), we use DESeq (multi-factor design) to normalize the raw data for math. modeling...class="preformatted">Dear All, The data set has 3 controls, and 9 treatments (transgenic biological replicates with different levels of gene expres…

convert DESeq convert DESeq

updated 13.7 years ago • Xin Davis

Hi all experts, I am very new in R and Bioconductor, so please be patient with me. I would like to do DE analysis for samples (without replicate) as a part of an RNA-seq project. As I read the R manual, firstly, we should estimate the dispersion value of samples using...and Bioconductor, so please be patient with me. I would like to do DE analysis for samples (without replicate) as a part of an …

estimate dispersion value edgeR Houskeeping genes

updated 9.4 years ago • Sara

preformatted">Hi Gordon and Bioconductor patrons, I have 6 experimental groups with 3 biological replicates each and I used the function estimateGLMTagwiseDisp to look at dispersion estimates for my data. When I plotted

updated 13.8 years ago • Alpesh Querer

anova for microarray data. In the 18 data files, have two time points and 3 treatments,and three replicates. Design looks like this Timepoint 4 5 4 5 4 5 treatment control 1 4 7 10 13 16 Mock 2 5 8 11 14 17 infected 3 6 9 12 15 18 Can

Microarray Microarray

updated 13.8 years ago • chawla

question into consideration. I have RNA-seq dataset, a time series experiment, 3 time points with 8 replicates each. I wanna check the variation in gene expression across time. But I want to take into consideration the surgeon

LRT deseq2 multiple factor design

updated 8.2 years ago • sally_b86

div class="preformatted">Hi , I have RNA-seq count data for 30,400 genes across 6 conditions (3 replicates per condition). I was trying different normalization methods and then test for differentially expressed genes

Normalization Normalization

updated 15.1 years ago • Shreyartha Mukherjee

a time-series microarray data generated with Yeast 2.0 chip. There are 30 time-points with no replication. Is there any package I could you to: - identify genes with significant expression changes through the 30 points

Microarray Microarray

updated 17.0 years ago • Paco Recca

RNAseq data generated previously. Basically, the dataset is made of 3 conditions, with 4 biological replicates in each condition, and 2 technical replicates per biological condition (maybe the best choice, but the data is here...metadata, design = ~Experimental_condition)` and then do `ddsColl <- collapseReplicates(dds, dds$Replicate, dds$Sample_name)` to merge technical replicates, and pr…

DESeq2

updated 23 months ago • theophile

Hi, I have timecourse microarray data generated from cell culture experiment. Three replicates were taken from the culture (three biological replicates - R1, R2 and R3), and, further on each replicate three treatments...were harvested at 12hrs, 24hrs, 48hrs and 72 hrs (H1, H2, H3 and H4, respectively). For all the replicates there was a common starting point of 0hrs without any treatment. FileN…

timecourse limma

updated 10.5 years ago • Sandhya Pemmasani Kiran

First I would describe my experiment design, I have two groups, GroupA and GroupB. Group A has 39 replicates (Biological), and Group B Has 77 replicates. The samples are human blood samples, collected and processed randomly

DESeq2

updated 3.3 years ago • MAHESH

as an outlier in the expression of some genes but looks congruent with the expression of the other replicates when I consider a large number of genes. !![In the pic you can see one of the biological replicates acting as an outlier

DESeq2 results Heatmaps plots

updated 3.2 years ago • Chiara

<pre> Hi all, I am working on ATAC seq data set, two cell types and two conditions, replicates >= 3 . read.csv2("SampleSheet041217.csv") diff <- dba(sampleSheet="SampleSheet041217.csv") diff_count <- dba.count(diff, minOverlap=2) 20 Samples, 649843 sites in matrix: ID Tissue Condition Treatment Replicate Caller Intervals FRiP 1 4471_64502 CD…

atac-seq diffbind

updated 8.7 years ago • zhaolin20042008

correspond to four different types of promoters and each of the four promoters has a biological replicate so totally there are 8 columns. I tried using the Limma package to find the differentially expressed genes across...several promoters ( with replicates) and I always get an error as Iam new to r and unable to understand it fully . This is the code that I used: Group <- factor

limma limma

updated 13.2 years ago • Guest User

<div class="preformatted">Hi All, I have two color microarray data (genepix format) from patients with cancer. I have a variable number of replicates per patient and in some cases a dye-swap. On each slide we compared the RNA from tumor tissue to RNA from healthy tissue...two color microarray data (genepix format) from patients with cancer. I have a variable number of replicates per patient…

Microarray limma Microarray limma

updated 18.6 years ago • Yair Benita

Hi, We have a three factor RNA-Seq experiment result from 167 samples (6 replications per sample). Factor 1 = salinity, level = 2 (fresh water, salt water) <pre> SALINITY <- c(rep(rep(c("FW","SW"), each=6), 7), rep(c("FW","SW...Hi, We have a three factor RNA-Seq experiment result from 167 samples (6 replications per sample). Factor 1 = salinity, level = 2 (fresh water, salt wat…

edger independent filtering multiple factor design cpm

updated 8.2 years ago • teshome.dagnem

<div class="preformatted">In my version of siggenes, I don't see any variables called x and y that can be passed to the function sam. If RG.all contains all the data you wish to compare, you only need to pass this data.frame along with a vector of classlabels that identify which class each column of data belongs to. If you are doing a two-class unpaired analysis, this will be a vector of 0s…

Microarray Cancer siggenes Microarray Cancer siggenes

updated 22.1 years ago • James W. MacDonald

a samplesheet.csv describing my samples and it looks like this: SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks,P eakCaller meio.1,meiocytes,H3K4me3,N,1,M_meiocytes_H3K4me3.bam,InM_input_meiocyt...gt;H3K4.B73 2 Samples, 38870 sites in matrix (45304 total): ID Tissue Factor Condition Replicate Peak.caller Intervals 1 meio.1 meiocytes H3K4me3 N 1 …

DiffBind DiffBind

updated 12.3 years ago • Anitha Sundararajan

here. I am using DEXSeq to analyse exon usage across 27 different human tissues. Each tissues have 3 replicates and some of them have 2 replicates. The error came out when I want to EstimateSizeFactors: <pre> > dxd = estimateSizeFactors

DEXSeq DESeq2 dexseq deseq2 alternative splicing

updated 10.3 years ago • Fahmi Nazarie

right and that I can rely on the output for the analysis. The summary of the experiments: I have 4 replicates of infected cells with Cryptosporidium and 4 replicates of control (uninfected) <pre> rawdata <- read.csv("celldata.csv

rnaseq edger differential gene expression

updated 9.8 years ago • MEM

Hi, I'm about to analyze ATAC-seq data for the first time and my approach atm is: 1. Calling peaks 2. Merge the narrow peaks files into one 3. Convert the merge bed to saf format for input in featureCounts 4. Using featureCounts (Rsubread package) to get counts 5. Use the counts as input to DESeq2 The thing is that I'm stuck at step 4. Since I cant make sense of the output I get. If I try …

Rsubread atac-seq narrowpeaks featurecounts

updated 8.1 years ago • j.bergenstrahle

Hi, I was trying to replicate the BHC library example code (https://bioconductor.org/packages/release/bioc/html/BHC.html) with the Beast Cancer...that, since my data is continuous, it should be discretized (as it is done in the 3rd example), so I replicate that part of the example: BiocManager::install("BHC") library(BHC) library(RCurl) library(factoextra) brea…

bhc error

updated 5.8 years ago • pavel.granalacant

of the disease. Therefore, each diseased sample from each patient supposed to be different with no replicates. So the phenotype looks like this</span> Sample.ID (Unique)  |  Patient (1:12) | Tissue\_Type (Diseased or Healthy...tissue. To overcome that I treated all the healthy tissues from different patients as biological replicates and given them the same label H. As for…

limma voom

updated 9.9 years ago • ea1402

I have a question about which analysis to do in LIMMA. I did three experiments (three biological replicates) each with one treatment microcosm ("L") and one control microcosm ("D"). For each experiment, I sampled both the treatment...and control microcosms at 5 time points (0 hr, 2 hr, 6 hr, 12 hr, 24 hr). With 3 replicate experiments * (1 treatment + 1 control) * 5 time points, I have data from …

limma limma

updated 12.2 years ago • Lauren Sassoubre

is at least a couple of releases out of date. As you may have realized, your experiment has no replication. If you want to ignore the time points (treat them as replicates), then your experiment reduces to a simple two group...to compare the whole group (WT) against the > other group (KO) considering the time points as replicates. > > > > -- output of sessionI…

edgeR edgeR

updated 13.2 years ago • Gordon Smyth

reads, male: no signal >> >> Condition 2: >> replicate 1: 3,102,608 good reads, male: 5.0 >> replicate 2: 3,451,983 good reads, male: no signal >> replicate 3: 2,892,192 good reads...NaN >> geneID: 38959 >> >> Raw data: >> >> Condition 1: >> re…

Normalization limma edgeR DESeq Normalization limma edgeR DESeq

updated 14.2 years ago • Nick Schurch

Hi all, I have a situation like WT, KO, WT+DRUG, KO+DRUG (5 replicates each). The initial idea to do the pair wise comparison and i did it. I have the results for WT vs KO and WT+DRUG, vs KO+DRUG

DESeq2

updated 3.3 years ago • barrypraveen

Dear Support, I am having "issues" with regards of performance of the normalizePlates function My current setup: I have 100 plates (384 dimension; replicate = 1; channel = 1) of a screening campaign and I would like to use BScore as we are facing side effects on the plates. I am using...performance of the normalizePlates function My current setup: I have 100 plates (384 dimension; rep…

cellHTS2 Normalization

updated 4.1 years ago • liebi83

pre> when I using DESeq with my samples(3 replicates each 2 conditions) ,I found that the padj of my final result are always 1. And the pval is normal varying in 0.01-1 .</pre

deseq

updated 10.7 years ago • 15150688610

div class="preformatted">Dear List, I have a time course experiment with three time points and 5 replicates for each time point. I want to get an expression profile from this data, and get the differential expression for

updated 20.1 years ago • Khan, Sohail

be divided into two groups, which then could be divided into two subgroups. And each subgroup has 8 replicates. I am writing to ask if someone can give me a small example of the data that could be red in edgeR. I would appreciate

edgeR edgeR

updated 13.7 years ago • Wang, Li

<div class="preformatted">Hi, I have replicate sample counts for 2 groups but one sample is 4x number of mapped reads Than the other samples. 528,428 625,889 498,569...div class="preformatted">Hi, I have replicate sample counts for 2 groups but one sample is 4x number of mapped reads Than the other samples. 528,428 625,889 498

edgeR edgeR

updated 14.2 years ago • Lana Schaffer

I want to analyze RNA-Seq with multiple samples with replicates. So I have two groups A & B and within that I have 5  different sub groups in each (a,b,c,d,e & a1,b1,c1,d1,e1).There

RNA-Seq

updated 8.9 years ago • minie

data I got has tumor/normal ratios of thousands proteins, and both tumor and normal have a number of replicates. Could such data be analyzed with limma? If limma can not be used here, what statistics method is suitable so that

Microarray Proteomics limma Microarray Proteomics limma

updated 13.5 years ago • Yong Li