Bioconductor Forum

for 24 samples, half of them human culture, half of them human mixed with mouse.  (Also, three replicates each with 4 treatments) For the mixed ones, about 50% of the counts map to mouse genes.  I don't believe the submitters

deseq2

updated 7.1 years ago • swbarnes2

genes. My question is what does PC1 represent. I was comparing a test to control only with 8 replicates each. Thank you in advance

pcaexplorer genespca deseq2

updated 8.1 years ago • sally_b86

as well as RPKM values stored in an excel sheet. I have two cell types, two treatments, and two replicates for each group and I am trying to get a DE result file and generate a volcano plot. I have the end of the process figured

deseq2

updated 5.7 years ago • zal4002

Hi,  I have 10 strains with three replicates grown under the same condition. I would like to perform  pairwise comparisons between the 10 strains without

deseq2 bioconductor rnaseq

updated 9.3 years ago • pkachroo

I have 30 paired-end samples with 6 replicates in 5 groups (4 treatments + 1 baseline control). I am trying to decide how to setup the DE analysis. The glm approach...I have 30 paired-end samples with 6 replicates in 5 groups (4 treatments + 1 baseline control). I am trying to decide how to setup the DE analysis. The glm approach would

edger rna-seq

updated 9.2 years ago • es874

packages doing Mixed-Model Anova that deal with unbalanced design, i.e. not the same number of replicates for each treatment- genotype combination. I am particularly interested in the interaction between treatment

Microarray Microarray

updated 21.9 years ago • Christian Landry

and summary, and loess for the normalization). My data set contains two factors and 3 technical replicates. One factor seems to be very strong (lots of effect) whereas the other is rather weak. thanks for any advice, +regards

Normalization affy Normalization affy

updated 21.5 years ago • Arne.Muller@aventis.com

I conducted my DESeq analysis on 30 samples split between 2 genotypes, 5 time points and 3 replicates (30 samples total - 15 per genotype). I tried to make my PCA plot but I seem to be missing 2 points ( 1 from each genotype

deseq2

updated 5.4 years ago • pthom010

of mine which is how to best measure the signal to noise ratio. also, how do you decide how many replicates are required for an experiment with out knowing (there is no way of knowing right?) what the variance will be? -isaac

updated 21.8 years ago • Isaac Mehl

2-way ANOVA design? Eg. we are looking at 8 treatments x 4 doses, with unequal numbers of replications within the groups. I really need the stepwise calculation, as I would try to put it in my own code (possibly in Visual

updated 22.2 years ago • Subramanian Karthikeyan

global) if arrays have different layout(different location and different number technical replicates (number of spots of a gene on an array))? Sincerely, Natalia.</div

Normalization limma Normalization limma

updated 20.6 years ago • NATALIA F TCHETCHERINA

input file on one graph? For example: CCPlot seems to have all samples and only have 1 legend replicate. My sample sheet and the plots generate can be downloaded from here: [https://1drv.ms/f/s!Aiu\_09KS3rmGi3zTZVMoE7X2nZIQ

chipqc

updated 8.5 years ago • C T

I've been using DESeq2 to compare two experiments, each with 3 biological replicates. I read in a Counts Table generated from Salmon. I've been doing this successfully for awhile, but my most recent...I've been using DESeq2 to compare two experiments, each with 3 biological replicates. I read in a Counts Table generated from Salmon. I've been doing this successfully for awhile, but my most re…

DESeq2

updated 3.0 years ago • vanbelj

differential peaks in condition1 versus condition2. I only have bigwig / bedGraph files of two replicates (condition1) and two replicates (condition2) (I do not have access to bam / fastq files). Considering these 4 samples

DESeq2 edgeR

updated 3.2 years ago • Bogdan

However, recently in the new limma manual appears that the block option should be used for technical replicates, and you need to calculate duplicateCorrelation. As far as I understood using block argument alone in lmFit you...arrays in limma. I have the impression that paired experiments are clearly different to technical replicates. So, I would appreciate if anybody can tell if I should use dup…

limma limma

updated 20.8 years ago • Pedro Jares

to analyse different expression of miRNAs, where I am comparing two treatments, 1 with 2 biological replicates and the second with 2 biological replicates I have followed the vignete, read the files, made raw.cat and filtered

HTqPCR HTqPCR

updated 15.6 years ago • Andreia Fonseca

hopefully a quick answer in reply.... I have data from Agilent bovine chips. Are the spike-in probe replicates (of which there are 32 on each chip) supposed to be highly replicable on an MA plot? Some of my chips show good reproducibility

updated 16.7 years ago • Nathan.Watson-Haigh@csiro.au

placebo/treatment) with >5 time points. >The main issue I encounter is that the number of replicates at each time >point is not the same: >time ttt placebo >t0 2 7 >t3 3 6 >t7 3 6 >t14 2 5 >t28 5 4 > >I tried to use...the timecourse package but obviously I can't set the required >replicate matrix. >Unless I…

TimeCourse limma timecourse maanova TimeCourse limma timecourse maanova

updated 18.0 years ago • Naomi Altman

78 78 148 124 3119s00202.1 33 68 168 198 3119s00232.1 52 73 135 99 CR1 and CR2 are replicates of controls and MR1 and MR2 are treated sample replicates library(edgeR) library(limma) raw.data <- read.delim

edgeR DESeq edgeR DESeq

updated 14.1 years ago • Avinash S

<div class="preformatted">Hi, I'm trying to do an analysis of some tag3 Affy microarray data with the limma package, and I've run into a problem I'm not sure how to solve. The data comes from a series of arrays recorded at different time points. Each probe on the array represents a DNA tag from a yeast gene deletion library. There are several different time points and technical replicates…

Microarray Preprocessing Regression Yeast probe affy limma Microarray Preprocessing Yeast

updated 17.2 years ago • Alex Gutteridge

internal outlier detection and replacement algorithm that requires a specified (I think default is 7) replicates. I have around 200 paired samples, ~100 pre and ~100 post treatment. In accordance with the paired multi-factor DESeq2...and outlier replacing methods. Is the inclusion of pairing making DESeq2 think that I have no replicates? How can I keep my paired design but still take advantage of…

deseq2 differential gene expression multiple factor design paired design

updated 8.9 years ago • gregory.l.stone

Hello All, I am trying to use DESeq, a sample of my data looks like below (X.1 & X.2 are replicates, Y1 & Y2 are replicates). *GeneNo X.1 X.2 Y.1 Y.2* gene00001 4 3 3 1 gene00002 17 45 39 30 gene00003 25 40 29 24 gene00004

DESeq DESeq

updated 13.8 years ago • OD

using the complete data due to increased sample size, or is it influenced by the fact that I have replicates within subjects (not really replicates, since they are treated) that the model does not handle? Any thoughts on how

rnaseq rna-seq differential gene expression differential expression edger

updated 10.0 years ago • Leif Väremo

I was concerned that the M value for some of the array features did not equal to the average of the replicates, even though it's supposed to. This is only seen with features if a pair of its dyeSwap measurements had a "NA" value...a dyeSwap pair gave a "NA" value for the feature, the M value would still be equal to the average of replicates as it's supposed to. This problem seemed to be caused by…

limma limma

updated 20.9 years ago • xiaocui zhu

500px"> <thead> <tr> <th scope="col">Category</th> <th scope="col">Condition</th> <th scope="col">Replicates</th> </tr> </thead> <caption>Experimental design</caption> <tbody> <tr> <td>Control</td> <td>Solvent 1</td> <td>2</td> </tr> <tr> <td>Control</td.…

deseq2 differential expression immunoprecipitation

updated 9.4 years ago • snamjoshi87

gt; A. Error: could not find function "dispersionPlot" > > B. dend.rep<-csDendro(genes(cuff),replicates=T) > > Error in csDendro(genes(cuff), replicates = T) : > > unused argument(s) (replicates = T) > > C. mCount<-MAplot(genes

updated 13.5 years ago • Jack Luo

it is the best way of doing it. Just copy the range, instead of downloading ORFik if you want to replicate this: library(ORFik) # If you want to replicate, just copy the GRanges object, instead of downloading ORFik # If you want...to replicate with ORFik use github devel version: devtools::install_github("ORFik/master") library(Biostrings) require(BSgenome.Hsapiens.UCSC.hg38

circulargenome ORFik getSeq

updated 4.8 years ago • hauken_heyken

knockdowns. Three conditions - Control, si1 and si2. Four doses - D0, D1, D2 and D3. There were no replicates. Total 12 samples. We are trying to use edgeR to identify differentially regulated genes. Since edgeR doesn't give...p-values without replicates, we took samples coming from D0 as replicates i.e. Control-D0, si1-Do and si2-D0 (This decision was taken based on our

edgeR DOSE edgeR DOSE

updated 12.5 years ago • Sandhya Pemmasani Kiran

I have two batches that have one sample in common, plus other samples in each batch. There are 3 replicates for each sample. Is there a way to compare other samples across tthe two batches? In other words, how can the batch

DESeq2 DifferentialExpression RNASeqData BatchEffect

updated 11 months ago • georgeyu703

Hello there, I am using NOIseq package, for analyzing RNAseq data without biological replicates. I got the output as well but I am not clear about the probability column in the output. It says that it gives the probability

RNAseq RNASeqData NOISeq

updated 3.6 years ago • Pratibha

lt;- estimateDispersions(dxd, quiet=FALSE) dxd <- testForDEU(dxd, reducedModel=~sample + exon + replicate:exon

DEXSeq rnaseqDTU

updated 4.4 years ago • rbenel

for a certain condition and running the omics experiment, I would use the mean cell count of my bio replicates to normalize to. But I'm not sure what the base function for this would be? Perhaps there's already a package available

normalization normalize cell

updated 7.6 years ago • bhgyu

I'm guessing the grouping has to take into account the originally supplied files (before replicate merging and sample reordering) but it would be nice to have a confirmation before doing DGE with mixed up sample

CAGEr

updated 4.7 years ago • MatteoP

<div class="preformatted">Hello all, I am sorry for this, but I need to retract my request for help. I am not sure LimmaGUI can cope with replicates in the same block (as this gal file shows). I was not expecting them to be in the same block and am getting the files checked...I am sorry for this, but I need to retract my request for help. I am not sure LimmaGUI can cope with replicates in …

limmaGUI limmaGUI

updated 20.6 years ago • Brooke-Powell, Elizabeth

My RNA-Seq experiment is comprised of two technical replicates each of a normal and affected phenotype across four time points (yielding 16 samples). My understanding

ebseq ebseq-hmm rna-seq

updated 10.2 years ago • vieuphoria

working fine except I'm not sure what the out put means. I have sample A and samlpe B on an array (3 replicate slides) and in limma analysis I put sample A as the reference. Therefore the results I get, are they the genes up/down

limma limma

updated 20.9 years ago • Josephine

I have three samples of dataset, a reference and two replicates for 1 hour and 24 hours. In each sample the gene IDs are arranged differently and the number of genes per sample...I have three samples of dataset, a reference and two replicates for 1 hour and 24 hours. In each sample the gene IDs are arranged differently and the number of genes per sample are

normalization

updated 9.5 years ago • humberto_munoz

div class="preformatted">In replicates of 3, I have a set of control and 4 treatment arrays. My question is, do I normalize (via rma) using all of the arrays at

updated 22.6 years ago • Leanna House

Hi, I have a little confusion while running DESeq2 (I have 2 conditions and three biological replicates). some genes display NA for p and p adjusted even though other values such as base mean and log2 fold change are all

geneexpression

updated 10.4 years ago • timarogger

I am trying to look at differential protein expression between multiple sample types with biological replicates for each type. Data was generated using nanostring DSP geoMX and normalised in-house. I haven't been able to find

R Differential expression

updated 5.6 years ago • james.monkman

dba_', ext='RData', bMinimize=FALSE) #' Create Report. ChIPQCreport(experiment,facet=T,lineBy=c("Replicate"),facetBy=c("Condition","Factor"),reportName=paste0(opt$name,"Marks",collapse = "_"), reportFolder=opt$name,colourBy=c("Replicate...calling for input ... <pre> dba.show(dba_chip) ID Tissue Factor Condition Treatment Replicate Caller Intervals 1 L13S13 MCF1…

diffbind

updated 8.3 years ago • ZheFrench

nbsp;                           "Replicate"), +                        row.names = c("Strain", "Time", "Replicate")) > phenoData <- new...nbsp; &gt…

betr timecourse

updated 9.6 years ago • Quang Nguyen

a Genechip experiment, with four time points and three >treatments (A,B and Ctrl), with no replicates. Am I correct in assuming that your first 4 chips are hybridised with Ctrl, the second four with A and the last four...matrix correct? No it's not. If my assumptions above are correct, and your time points were really replicates, which they're not, then you'd want either > desig…

Microarray Normalization limma Microarray Normalization limma

updated 22.4 years ago • Gordon Smyth

due to the delicate structure of the brain and funding, we do not have the capacity for biological replicates. So far this has been fine for comparison at brain tumour cohort level, comparing the expression of multiple brain...vs 4 normals comparison in order to get p-values. This is essentially a thought to mimic biological replicates based on similarity of expression profiles of Tumour samples…

GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod

updated 2.1 years ago • Manthos

gt; differentially-expressed genes (highest B = 3.1). > > I'm using three biological replicates, each hybridised to two dye- swapped arrays > as technical replicates, on Compugen human 19k cDNA slides. > > Is

limma limma

updated 20.5 years ago • Gordon Smyth

<div class="preformatted">Hi, I was hoping someone would be able to provide me with some general advice on using EdgeR for some sRNA datasets I have received. I have 3 sRNA datasets, and I have calculated all abundances (just read counts) of every sequence in each dataset. Unfortunately, there are no replicates. The goal is to find specific sRNA sequences that are higher in abundance in d…

Normalization edgeR Normalization edgeR

updated 12.4 years ago • Kenlee Nakasugi

slightly unconventional dataset to try. We have two groups to compare (life stages) each with three replicates. But, for each sample in each group, we made two different RNAseq libraries. 1) one from fragmented mRNA (classical...efficience of that gene. We can generate these efficiences (ratios) for each of the three replicates in each group. Can I feed this data to edgeR to find out which gene…

RNASeq edgeR RNASeq edgeR

updated 12.7 years ago • gowtham

trying to see differential expression of genes across my samples ( control, T1, T2, T4) and I have 1 replicates for each, i.e. I have 8 samples in total. I did the transcripts count from Htseq and now while trying to compare between...each timepoints ( control vs T1, control vs T2, control vs T4). Also I want these separate for both replicates. Till now my code looks like this:   direc…

rnaseq deseq2

updated 8.2 years ago • AP

245, 255)">I am analyzing RNAseq data to study DEGs in two diffrent conditions. i don't have any replicate for my samples. tophat->cufflinks->cuffdiff pipeline is completed and now i want to plot graphs using cummeRbund...E:/cuff\_out/read\_groups.info</span> <span style="background-color:rgb(245, 245, 255)">Writing replicates Table</span> <span style="ba…

cummerbund readCufflinks

updated 10.1 years ago • Pinal

<div class="preformatted">Dear All, While looking at the Limma user guide, I came across the following example > targets <- readTargets("SwirlSample.txt") > RG <- read.maimages(targets$FileName, source="spot") > RG$genes <- readGAL() > RG$printer <- getLayout(RG$genes) > MA <- normalizeWithinArrays(RG) > MA &…

limma limma

updated 20.7 years ago • Ankit Pal

Note: I do not have biological replicates. I have read the warning messages and am aware that the analysis without replicates probably will not yield

deseq2 differential gene expression design

updated 7.2 years ago • newbio17

BioC users I am working with affymetrix exon array data of 40 samples with 8 different groups and 5 replicates of each. Two different strains are used in this study. Cells were cultured for either 3 days or 7 days. At 3 days the...SVA BLA Drug B treated mature SVB BLB *each has 5 replicates I would like to compare the effect of different drug tre…

sva sva

updated 12.7 years ago • sanj

I am trying to compare two different conditions (with 2 replicates each) using Diffbind. For my Diffbind output, I'm getting 0 counts for one of the conditions and high counts for the

DiffBind

updated 3.0 years ago • slrpatty

<div class="preformatted">I have previously used DESeq to analyse differential binding in ChIP- seq data (2 replicates of two ChIP samples). I believe the newer versions of DESeq (i have 1.6.1) are able to consider the matching input samples...preformatted">I have previously used DESeq to analyse differential binding in ChIP- seq data (2 replicates of two ChIP samples). I believe the n…

DESeq DESeq

updated 13.9 years ago • Ian Donaldson

4 different stimuli for 1 specific cell type, and for each stimulus I have three biological replicates. I'm looking for a way to analyze the expression data of the various cards, preferably in R/BioC. Any experience/suggestions

updated 17.4 years ago • Bas Jansen

data using the HTqPCR package. I have all my data in an excel sheet (approx. 350 samples and their replicates).  Each row is a sample and each column states the gene, treatment, Ct values, etc. How do I load this information

htqpcr

updated 9.8 years ago • Pheebz

I am looking for references to published papers on microarrays which mention duplicate spots, i.e., replicate spots on the same array containing the same probe. The treatment of the duplicate spots can be very brief, e.g., just

probe probe

updated 21.9 years ago • Gordon Smyth

for a time-course experiment. I have 7 time points (0,3,6,9,12,24,27 hours) with three technical replicates at each time point. Cy3 is the untreated, Cy5 is the treated sample on each chip. There is an example in the limma user

limma limma

updated 17.6 years ago • Endre Sebestyen

Hi I have some .txt files of RNA seq data form an experiment with 3 groups with 3 replicates each of which has the same features including genes ID and read counts.  How can I make expression set from...Hi I have some .txt files of RNA seq data form an experiment with 3 groups with 3 replicates each of which has the same features including genes ID and read counts.  How can I …

RNA seq anaylsis R

updated 8.9 years ago • Isadeghi66

Hi all I am working with biological replicates and I am a bit worried about the biological variation between samples. For example, the abundance of a certain

biologicalreplicates statistical test

updated 9.3 years ago • Yogi Sundaravadanam