Bioconductor Forum

0.000 1265.967 For the rest of the genes the values are pretty consistent in each pair of replicates. I thought that this gene won't be considered significantly changed, but in fact it shows up in the result as significant...DESeq that will help to increase the stringency of the analysis and exclude these genes, or with two replicates there is nothing that can be done? Thank you in advance…

deseq2

updated 5.8 years ago • ninova

and interactions for a 2x3 factorial RNA-seq project we have been running (we have reasonable replication: 7 biological replicates per treatment combination, i.e. 42 libraries in total). >From our reading of the edgeR

edgeR edgeR

updated 12.1 years ago • Guest User

group. arrayWeights allow me to get very interesting results but in documentation it says you need replicates. Are they technical or/ and biological replicates? I couldn't find clearly the information. My second question is

probe limma probe limma

updated 13.5 years ago • Amos Kirilovsky

834 9 YM_E3 YM 1094 10 YM_E4 YM 1313 11 YM_E5 YM 2643 ``` I have 6 replicates for OM group and 5 replicates for YM group. I am using a second factor which is numeric (taille). I checked that colData

deseq2

updated 6.2 years ago • emilie.derisoud

some RNA-seq time series data. I have four time points. The first and last time points have three replicates, while the middle two have two replicates. The following gives the error I get: require(edgeR) counts <- read.csv

edgeR edgeR

updated 14.9 years ago • Colin Maxwell

by different batches. Say, we have multiple groups (A, B, and C) with 2 conditions (X, Y) and 3 replicates for each. We'd like to list DEGs between condition X and Y in each group, and plan to do some posthoc analysis. Group...conditions, and we came to know that group was prepared differently, say in batch 2 and 3. Group-replicate-Condition-batch A - 1 - X - batch1 A - 2 - X - batch1…

DifferentialExpression DESeq2

updated 5.0 years ago • gairoju

I have a simple loop of 2-color cDNA microarray experiments containing 6 individuals and 2 technical replicates for each. After batch and printtip normalization I need the intensity values for each feature, for each individual...design, not a reference design, I would like to obtain intensity value estimates for all biological replicates. Is there a way to get normalized intensities for all indiv…

Microarray Normalization Microarray Normalization

updated 17.6 years ago • Lin Huffman

Array7 State2 Ref Array8 Ref State2 Array1 and Array2 are technical replicates but dye swapped. Similarly the other pairs of slides are dye swapped technical replicates. The design matrix would...and below have been weighted zero. Further analysis was done as mentioned in section 8.2 'Technical Replication' and section 8.4 'Two Groups: Common Reference' of LIMMA u…

Microarray Normalization Microarray Normalization

updated 17.5 years ago • Arun Kommadath

we can help with our design. Currently, we are getting errors. We have 18 RNA-Seq biological replicates (samples), each sample has two columns of counts for each tag, one for the maternal allele and one for the paternal...lt;-factor(c(rep(title, 18))) parent1<-c("father", "mother") #parent labels for the first nine replicates parent2<-c("mother", "father") #parent labels for t…

edgeR edgeR

updated 13.6 years ago • Christopher T Gregg

gt; DBdata1 6 Samples, 5111 sites in matrix (7058 total): ID Tissue Condition Replicate Caller Intervals 1 P359 SF Hotair 1 bed 4637 2 cP359 SF Unstim 1 bed 4313 3 P361 SF Hotair 1 bed 5100 4 cP361 SF Unstim...evaluation > DBdata2 6 Samples, 5111 sites in matrix: …

Diffbind ChIPseq Affinity analysis Differentially bound sites occupancy analysis

updated 6.7 years ago • rapmic

table> I expected the log2fc to be -0.0892376619 I must say that this test is done without replicates, only one control sample vs its corresponding treament sample. Could this affect in some way?? When I perform the...same test with 3 controls and 3 treatments, used as replicates for the two conditions, the log2(fc) are correctly calculated. \*\*The control and treatment samples shown here…

deseq2 differential gene expression log2fc

updated 9.9 years ago • Osvaldo

WT, 4d, 4e), each strain has uninfected samples(PBS) and infected samples, (KPn) and 2-3 biological replicates for each sample I’ve corrected for background and normalized between arrays, using the quantile method, filtered...control probes and low expressing probes, and averaged replicate probes:   <pre> targets<-readTargets("Targets.txt") RawData<-read.maimages(…

limma microarray

updated 11.0 years ago • dsperley

Hi Aaron. I have Time-series bulk data (with two biological replicates for each time) and now I wish to use it to annotate my single-cell data. My Single-cell data contains two samples, One...Your `vignette` is quite straight forward but can you tell me how I combine two biological replicates per time point into one column so that I have one column for each time point and use it for assigning la…

SingleR

updated 3.8 years ago • rohitsatyam102

samples to Agilent chips. Our experiment is simply a comparison between two groups with 5 biological replicates per group (all 10 samples are biologically independent). From my reading, a multi-dye-swap and loop design both have...it could be extended more easily than a loop design in the future - i.e. add additional biological replicates at a future date? The idea behind the dye-swap is to get …

Microarray limma Microarray limma

updated 16.9 years ago • Nathan.Watson-Haigh@csiro.au

t perform differential analysis. The only thing I can think to do is set a threshold (i.e. all replicates must have > 10 gene counts) then say these are expressed. But I don’t think this is a very good way of doing it. Do you

RNASeq Gene ExpressionData

updated 4.2 years ago • AZ

My dataset contains mini-bulk samples (5 cells per sample). I have 6 replicates for each cell subset, meaning that I sorted 6 wells with 5 cells/well per subset. I've analyzed my data using the 'regular

deseq2

updated 6.1 years ago • gmpjverstappen

and C are three patients Would a paired t-test work better than one-way ANOVA here? Do I need more replicates? thanks for your help Yogi </div

updated 16.7 years ago • Yogi Sundaravadanam

Hi, I have three group RNA-seq data, each of them have three replicates: MCF10A (normal), MCF7 (Breast cancer) and MCF7-TamR (Tam Resistant). I was wondering if there is a way to design a differential

deseq2

updated 5.3 years ago • kf

millions of reads to the host but fewer reads of the parasite. My library size of parasite by replicate is around 193,000. I have seen that "As a rule of thumb, we require that a gene have a count of at least 10–15", given my low

cpm filtering transcriptomics rnaseq edgeR metatranscriptomics

updated 6.4 years ago • vm.higareda

Hi , I'm trying to perform rrbs dme analysis using edgeR on 50 samples (5 replicates per timepoint /sex). It seems to be running forever (>8 hours) and not produce any output. Design matrix has 50 samples

edgeR

updated 5.3 years ago • Archana

If only one out of five assays has replicate samples, is it possible to avoid specifying a sampleMap row for every column in every assay? Also, I notice assay...If only one out of five assays has replicate samples, is it possible to avoid specifying a sampleMap row for every column in every assay? Also, I notice assay columns

MultiAssayExperiment

updated 4.7 years ago • Dario Strbenac

expressed genes? If so, how can I extract this subset? I have 5 groups in my PCA with multiple replicates and extracting the subset of genes that drive the PCA result will be very useful. Also, is there a way to adjust the

deseq2 PCA

updated 10.3 years ago • sunil.mangalam

analysis. I have been trying to normalize 4 chips (two dye-swap experiments done in biological replicates) After doing backgroundCorrect(method="normexp") , one of the arrays has all of its $G values at NaN. This does not happen

Microarray Microarray

updated 20.8 years ago • Palmer, Lance

pvalues in the result from glmQLFTest. For example, I have 4 treatments A, B, C, D, each has 3 replicates, and I want to compare any treatment pairs, i.e.: A-B, A-C, A-D, B-C, B-D, C-D. I use a matrix, generated by "makeContrasts" to define

glmQLFTest pvalue

updated 7.0 years ago • zhang.jianhai

Hi, I am trying to replicate the case studies at the end of the edgeR user guide to verify a workflow I’ve developed. Particularly I am interested

edger

updated 5.8 years ago • ali.sajid.imami

a way to calculate within and between group variability between two sample groups (with biological replicates) within DESeq ? I went through DESeq manual, but couldn't find any reference.  So is the only way is to calculate

DESeq DESeq

updated 13.5 years ago • sudeep s

all, I have a matrix of "A"/"P" calls. I want to filter for the probes that are present on all the replicates, for example sample1_1 sample1_2 sample2_1 sample2_2 gene1 A P P P gene2 P P A P gene3 A P A P gene4 A A …

updated 14.8 years ago • Wendy Qiao

Hi I have two replicates for two conditions ( resistant and sensitive ) at two time intervals for conducting a Differential Expression

egder dgelist group rnaseq

updated 8.2 years ago • fawazfebin

Suppose that in my expression matrix I have 3 conditions: treatment A, treatment B, and control (2 replicates everywhere). Now my goal is to compare treatment A to control. My question is, should I do voom and further analysis

limma

updated 6.3 years ago • chipolino

nbsp;                   factor="ER",condition="wt",replicate=2) mESC <- dba.peakset(mESC, bamReads = "/home/tandrean/Desktop/mESC/3.sorted.bam",bamControl = NULL,     &nbsp...nbsp;                   fac…

Control Usage input files

updated 9.0 years ago • fusion.slope

Dear Dr. Stark, The following question has been asked before regarding error in dba.analyze step of diffBind when the contrast is set up for samples with no replicates. Obviously I should be comparing samples with multiple replicates but while I wait for more data from the sequencer it will be great if I could implement DiffBind for no replicates. When I run __dba.analyze step__, I get the foll…

diffbind

updated 10.8 years ago • danishm20

duplicateCorrelation Dear Devin, There are a couple of problems. Firstly, you've told us that your replicates are 112 spots apart, but you haven't told limma this. So the software is assuming that the replicates are side-by-side...to check that duplicateCorrelation() is getting the right input, the best way is to check that your replicates really are at the spacing you think they are. Your data…

Normalization probe limma Normalization probe limma

updated 20.2 years ago • Hua Weng

Hello, I have RNA-seq data from 27 samples to analyse. I have 2 differents treatments (Compound1 and compound 2) + control (DMSO) and I have 3 times. I have 3 replicates for each combination. I am trying to use DESeq2 to find the differentially expressed genes. First, may I double check...2 differents treatments (Compound1 and compound 2) + control (DMSO) and I have 3 times. I have 3 replicates…

deseq2

updated 10.8 years ago • AurelieMLB

div class="preformatted">Hi, I have 4 replicate slides. Within each slide, there are 3 replicate spots for each gene. After doing the within Array normalization

Normalization Normalization

updated 20.8 years ago • Yi Zou

and two time periods for a total of 10 different experimental conditions with 4-5 experimental replicates for each.  I'm using DESeq2 to analyze for DE of genes from RNAcounts. There are really multiple comparisons...is a concatenation of two treatments, 3 surgeries and two time periods (this is 10 groups of 4-5 replicates each, because time period 2 is missing one surgery).  …

deseq2

updated 9.6 years ago • jshouse

towards a pooled mean so in principle it should work. I used 7 genotypes, 2 treatments first with 3 replicates and then with just 2 replicates. For contrasts I compared each genotype untreated vs. treated (ebfit p<0.01). On

limma limma

updated 21.3 years ago • Matthew Hannah

Hello, I have an RNA-seq dataset consisting of 16 species, each subjected to three experimental treatments, with three replicate individuals each. The species fall into three physiological categories. I would like to identify genes whose response...seq dataset consisting of 16 species, each subjected to three experimental treatments, with three replicate individuals each. The species fall into t…

edger differential expression phylogenetic comparative methods

updated 8.6 years ago • noah.reid

1:4], groups = files$Treatment[1:4], calibrator = "Control") what to do bcz my samples have no replicate and groups consist of only 2 sample not 4 as in example file. every sample have 26 features(13 replicate) so how i perform

qPCR qPCR

updated 13.5 years ago • rakesh sharma

control) tested at 4 concentrations both with and without estrogen (E2). We had three biological replicates and three technical replicates per plate. We assigned samples labeled "control" to each chemical and assigned

deseq2 interactions contrast

updated 8.5 years ago • grashow

The figure above is derived from the code below ```r viewPathway("E2F mediated regulation of DNA replication", readable = TRUE, foldChange = geneList) ``` [1]: /media/images/dd6fa916-fe9e-403f-b17f-0f53a2c9

clusterProfiler ReactomePA

updated 3.8 years ago • charlesgwellem

I am trying to conduct a `differential expression (DE) analysis` to identify enriched peptides in a `phip-seq` analysis using `edgeR`. However, as there are no replicates available, I am uncertain about how to determine the reliability of the ***BCV (square-root dispersion)*** utilized in...to identify enriched peptides in a `phip-seq` analysis using `edgeR`. However, as there are no replicates a…

edgeR

updated 2.8 years ago • f_rahmdani

to 0 it's fine. But now i'm not sure if i should use a different cutoff instead of 0. I have 3 replicates per sample

deseq2 up-regulated down-regulate

updated 6.7 years ago • anaQ

7 week , 9 week  * 4 different tissue: embryo, endosperm, mesocarp, pericarp * 2 biological replicate for each Regards Yogesh

deseq2

updated 9.3 years ago • nabiyogesh

preformatted">How does the vsn method compare to rma, in terms of bias and the variance between replicates? Has anyone applied both methods to a standard dataset and compared the results? Thanks, Tom Price ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Thomas S. Price

Genetics vsn Genetics vsn

updated 23.1 years ago • Tom Price

Hello, I did plotcounts shows normalized counts for a single gene. two groups contains two sample which are not close together  actually they are not replicates indeed, but the same library sequenced on two lanes. so I would appreciate let me know about such cases  how should...single gene. two groups contains two sample which are not close together  actually they are …

deseq2

updated 7.3 years ago • lkianmehr

Hi all, I analysed the list of DEGs in 10 tumour-normal pairs (without replicates), with edgeR. I used the paired design <pre> design = model.matrix(~Patient+Tissue)</pre> Now, I would like to get the list

edger degs paired design

updated 7.6 years ago • takumima

Hi All, I have 2 control and 2 treated replicates. I am running DESeq2 in order to identify differential bound regions form ChIP-seq samples. However, their are...Hi All, I have 2 control and 2 treated replicates. I am running DESeq2 in order to identify differential bound regions form ChIP-seq samples. However, their are discrepancies

deseq2 chip-seq Differential binding

updated 9.6 years ago • p2016k

in the comparisons. Is it OK to use DiffBind / csaw to compare these two ChIP seq samples (with replicates of course)? Thanks

DiffBind csaw

updated 5.6 years ago • GFM

only raw read counts of RNA-seq. The design was quite weird. They applied the same procedure to the replicates but got sequenced in completely different platforms(Solid, Nextseq and Hiseq). If the procedures from fastq files

deseq2

updated 7.7 years ago • krisd3v

Hello, I would like to identify deferentially expressed genes. I have 50 different individuals in three biological replicates (50 x 3=150) and they are not challenged for any condition (for e.g. control vs wild). I mean there is no treated vs non-treated...like to identify deferentially expressed genes. I have 50 different individuals in three biological replicates (50 x 3=150) and they are no…

edger

updated 9.9 years ago • myprogramming2016

Hello, I have RNASeq data from 4 groups with 3 biological replicates. The conditions are: 1) untreated, 2) treated with a drug, 3)infected with a virus, and 4) treated and infected. I am looking

edger

updated 6.5 years ago • sandraggava

Hello all, I have an array with 8 groups and 4-time points (3 replicates in each), with the exception of 1 timepoint where the rats died. Reading about this missing group on Limma guideline

limma

updated 5.0 years ago • ijvechetti

I wonder if anyone has experience doing an analysis with 3 biological replicates for the treatment but only 2 for the control? I am almost certain I screwed up one of my control samples during the

biologicalreplicates

updated 9.3 years ago • hac141

I know this question has been asked before, but even reading through older posts I cannot replicate the LogFC output in R.   design <- cbind(Grp1=1,Grp2vs1=c(0,0,0,1,1,1)) data <- 1:6 fit <- lmFit(data, design) fit <- eBayes

limma logfc

updated 9.7 years ago • cookm346

<div class="preformatted">Dear Guillaume, The first approach (using duplicateCorrelation) is correct. The second approach accounts for technical variability, but fails to fully account for biological variability of the wt-mu contrast in the standard errors of the tests. The second approach therefore tends to be anti- conservative, and will usually lead to more apparent differential expre…

limma limma

updated 15.0 years ago • Gordon Smyth

many significantly regulated genes (5 or so), which is likely due to the small number of biological replicates and the large diversity in the human population. I also tried another approach, leaving the individual labels...why there is such a large discrepancy between the two analysis methods. Is this due to the way replication is handled? Could anybody comment on the validity of these two anal…

BRAIN BRAIN

updated 20.4 years ago • Koen Bossers

Hi, I wanted to replicate the GO analysis done thru' (http://geneontology.org/), but using R/Bioconductor. For the 'original' GO analysis, I just...Hi, I wanted to replicate the GO analysis done thru' (http://geneontology.org/), but using R/Bioconductor. For the 'original' GO analysis, I just copy...and click on 'Launch'. This resulted in a set of significant GO terms. I am now trying to…

topGO Gene Ontology enrichment panther.db

updated 5.4 years ago • Brian Smith

trtR/trtNR) and the sampling is done at 7 different time-points. I have different number of replicates: for trtR two replicates and for trtNR 5 replicates for each time-points (some time number of replicate is more). I

deseq2 GLM timecourse

updated 8.2 years ago • rahel14350

Hi, I got an experimental design made of 3 replicates. Each replicate consists in a time course comparing the response of a cell line to a treatment "A" vs a placebo "B". Replicates...are not carried out on the same day, but within each replicate, treatment and placebo time course are carried out in parallel, usually starting from the cell line culture. Experimental...series spline model.ma…

design limma

updated 24 months ago • SamGG

the chromatin interaction differences between two conditions and I have more than one technical replicates for each condition. However, I have already the corrected matrices (with ICE and other methods) and I would essentially

diffHiC statistical test

updated 9.6 years ago • lazaris