Bioconductor Forum

nbsp;data-sets. In many forums and their manual also, they declared that if you do not have "any replicates", you should use __Fisher's exact test__ instead of __t-test__. I changed properly all the

methylsig no replicates dmr

updated 7.4 years ago • nilaycan

To: Federico Gaiti Cc: Steve Lianoglou; bioconductor@r-project.org Subject: Re: [BioC] Low number of replicates DESeq Then I would recommend the multifactorial design, as it's the best you can do without stranded replicates...overlapping antisense transcript on the other strand". Because for such transcripts, only the single replicate for the stranded experiments will contribute signal (if I am …

Transcription GO DESeq2 Transcription GO DESeq2

updated 11.8 years ago • Federico Gaiti

<div class="preformatted"> Hello- I am working with a metagenomic dataset in DESeq2 that does not have true biological replicates but has multiple factors and levels. Due to the difficulty in obtaining these samples, replicates were not an option. The study design consists of seawater microbes collected at 4 depths. For each depth, there are 3 treatments (live, dead and none). I expect the…

DESeq2 DESeq2

updated 11.9 years ago • Guest User

vs the non- treated samples, where each sample is a leaf from a particular tree. I have 5 biological replicates (5 treated and 5 untreated), and for each biological replicates- -- 2 technical replicates, which are dye swapped arrays...duplicated: on the left side and on the right side So...The experiment design involves 3 kinds of replicates: within array replicate (duplicate spots), technical r…

Microarray limma Microarray limma

updated 15.8 years ago • Staninska, Ana, Dr.

been given the microarray data to analyze for a 4 point time course experiment with two technical replicates (dye swaps) and no biological replicates. One channel is has RNA from a control mouse and the other has RNA from a mouse...do this with the given experimental design? I have only worked with Affymetrix chips with biological replicates, so this type of experimental design is new to me. If …

Microarray Normalization limma Microarray Normalization limma

updated 17.3 years ago • Matt Huska

the control probes were supposed to be removed. I have 38 arrays with 36 biological and 2 technical replicates. I?ve loaded the .txt files with RG <- read.maimages(). I normalized between arrays with vsn. I won?t go into the design...don?t think it?s relevant for my question. I?ve tried to include the information from the technical replicates by using duplicateCorrelation() and defined wh…

Microarray GO vsn limma Microarray GO vsn limma

updated 17.6 years ago • eldridb@stud.ntnu.no

the last three lines 18S is presented three times but I would like to have a average of the three replicates. qPCRraw= readCtData(files=c("palte_res.txt"), path = NULL, n.features = 384, flag = 4, feature = 6, type = 7, position = 3, Ct = 8, header

ddCt HTqPCR ddCt HTqPCR

updated 13.9 years ago • marco fabbri

class="preformatted">Hi Lukas, I have a question about the MEDIPS.createSet function with biological replicates. In the vignette, a MEDIPS.createSet command is issued for the first replicate of a set, and then other replicates...from one individual, so that I have to have a separate MEDIPS.createSet call for each biological replicate? This seems inefficient, because the BSgenome, uniq, extend…

BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS

updated 12.0 years ago • Vining, Kelly

3 B 11 3 C 12 3 D Each mRNA has 3 replicates (same y location and different x location), I am not a biology person, I hope I could express clearly. Now I want to compare

updated 19.0 years ago • Yanyan Li

times on each array. I know how to fit blocks as random as explained in the Limma manual (Technical replication I) I know how to account for the replication within arrays. Is it possible to fit random block effect and technical...replicates within array at the same in linear model using Limma ? Thanks Peter</div

limma limma

updated 20.5 years ago • Peter Sørensen (HAG)

www.biostars.org/p/345751/\#345776 Hello, I am trying to figure out how to handle biological replicates across batches in DESeq2's design matrix. They're not quite technical replicates, but trying to include the sample...instead. Using collapseReplicates() doesn't feel appropriate because these aren't really technical replicates - a whole new library was produced for the second batch, just usi…

deseq2

updated 7.1 years ago • kmuench

around the spacing issue by sorting the genes by name, but I'd like to account for both the on-chip replicates and the fact that file 1 and file 3 (and file 2 and file 4) are dye swaps of the same two samples .. *not*biological replicates...this time it is not possible to estimate correlations between duplicate spots and between technical replicates simultaneously. If 'block' is not null, then t…

probe probe

updated 16.7 years ago • Joseph Fass

Hi, this is my first time doing differential expression analysis and I have a few questions about the data output. My data was collected from 4 different cell lines derived from 4 different animals (as biological replicates). We are getting inconsistent calling of DEGs and I'm not sure why. Attached are a few scatter plots of the genes in question. For (B) it was called DEG even though it was …

DESeq2

updated 4.7 years ago • lnblock2

Patient_3_untreated, So for each condition (tread vs untreated), we have three biological replicates. I followed <4.4 RNA-Seq of oral carcinomas vs matched normal tissue> in edgeR User?s Guide to analysis these...My questions are: 1.Could I say that, especially basing on the result of MDS-plot, the biological replicates are not consistent in my case, or the quality (fitness for pu…

RNASeq edgeR RNASeq edgeR

updated 12.4 years ago • sheng zhao

<div class="preformatted">Hi A simple question really - I have five biological replicate RNA samples. Each will have cells untreated vs treated, so that's five arrays. I want to do dye-swaps, but that means I...div class="preformatted">Hi A simple question really - I have five biological replicate RNA samples. Each will have cells untreated vs treated, so that's five arrays. I want t…

updated 19.5 years ago • michael watson IAH-C

gt; able to find information about how to deal with the following issues: > > 1) technical replicates > We have two biological samples, two libraries (of different insert size) > were prepared for each of them. so...gt; > conds <- c( "Sample1", "Sample1","Sample2","Sample2") since they are only > technical replicates, not biological. But I'm not su…

RNASeq DESeq RNASeq DESeq

updated 15.6 years ago • Simon Anders

Hi, There has been quite a bit of discussion on this listserve about dealing with technical replicates (in sets of arrays where the gene layout is the same across the experiment). We have just started analysis of a Stanford...I would really appreciate any comments anyone may have on our thinking! (1) Averaging the technical replicates within an array Pro's: (a) they are the same DNA sequence o…

a4 a4

updated 20.2 years ago • Margaret Gardiner-Garden

Hello, I have the following dataset. ```r Sample Patient Condition Sample1 Patient1 Condition1 Sample2 Patient1 Condition1 Sample3 Patient2 Condition1 Sample4 Patient2 Condition1 Sample5 Patient3 Condition2 Sample6 Patient3 Condition2 Sample7 Patient4 Condition2 Sample8 Patient4 Condition2 ``` Samples from the same patient are biological replicates since they were taken from the same culture …

DESeq2

updated 4.4 years ago • S

data. For this analysis, I am using the Limma package. The experiment design involves 3 kinds of replicates: duplicate spots (within array replicate), technical replicates (as dye swap), and biological replicates. I know that...to treat this kind of experiment, but I have an idea how to avoid duplicate spots (within array replicates), if that is possible. So here I need your help. There are 8x4 …

Microarray limma Microarray limma

updated 15.8 years ago • Staninska, Ana, Dr.

stat.ethz.ch/pipermail/bioconductor/2003-December/003277.html >He has got 30 individuals with 4-6 replicates of each. This would mean >that 120 - 160 hybridizations have been done. The example targets file >that is given...Patient2 >... > >Here is were I get confused because it looks here as the technical >replicates are included in the targets fil…

limma limma

updated 21.7 years ago • Naomi Altman

17452 19469 21509 27042 isoform4 156 165 7 9 where CK-1 and CK-2 are replicates of the one condition, T-1 and T-2 are replicates of the other condition. When I try to find differential expression...DESeq2, I got the Warning: "Dispersion fit did not converge". Simon said when analysis data without replicates would arise this warning. But my data do have replicates, W…

DESeq DESeq2 DESeq DESeq2

updated 12.0 years ago • Jiewencai

C + the same 12 samples with condition B So, the 12 samples with condition B are technical replicates that have been profiled across the two batches. I'm actually not interested in condition B; I need to compare the...Bioconductor packages (or other methods/approaches) that will allow me to **use the 12 technical replicates profiled across batches to correct for batch effects** before perfo…

deseq2 ruvseq sva edger limma

updated 6.8 years ago • enricoferrero

also array effect. My main pursues are to get contrasts as I specified and account for technical replication (isolation). I think that I should include all of this effects. I'll try to use maanova package. Thank you, Best regards...suggested by > Naomi in some of her posts. > > Here is my targets with number of biological replication (replication of > entire schem…

limma maanova limma maanova

updated 15.7 years ago • Maciej Jończyk

From: Pita <pwilkinson_m@xbioinformatics.org> > Subject: [BioC] Using limma with contrast matrix ,replicate spots, > To: bioconductor <bioconductor@stat.math.ethz.ch> > > What is the significance of this error? What does

limma limma

updated 20.9 years ago • Gordon Smyth

<div class="preformatted">> Date: Thu, 2 Jun 2005 11:47:15 +0200 > From: Peter S?rensen (HAG) <peter.sorensen2@agrsci.dk> > Subject: [BioC] random block effect and technical replicates within > array at the same in linear model using Limma ? > To: <bioconductor@stat.math.ethz.ch> > > Dear list, > > I hav…

limma limma

updated 20.5 years ago • Gordon Smyth

genes. I have some questions about the design matrix and the handling of biological and technical replicates. The target file is: Sample_name sample_type sample_replicate disease_status MPM_07 1 1 1 MPM_08 1 2 …

Microarray limma Microarray limma

updated 13.6 years ago • Manuela Di Russo

you say there's a problem. duplicateCorrelation() has no difficulty with technical and biological replicates in the same experiment. >> >> You might analysis your experiment by: >> >> targets$Treat <- factor(targets...gt;> To: bioc-devel at r-project.org >>> Subject: [Bioc-devel] technical and biological …

Microarray Normalization Microarray Normalization

updated 13.5 years ago • Gordon Smyth

Hello Bioconductor community, I have 6 RNA bacterial libraries from 3 biological replicates (control and treatment). PCA analysis shows that one of the control libraries clusters away from the other 2 controls...purely based on the PCA plot, is correct, so I wonder if there's a way to correct for biological replication during the DE analysis?    Thank you

rnaseq

updated 8.3 years ago • hac141

not the difference between the patients. The problem is how to deal with different levels of replicates and how to create a correct target file since I have no common reference? This is how the experimental set-up looks...as long as the original MA object. For the patients with two biopsies I averaged over the technical replicates (dye-swaps) and put the values from biopsy one and then the values…

limma limma

updated 21.7 years ago • Johan Lindberg

Hi, I have RNA seq data for 7 time points with 3 replicates each, I would like to mark genes that are differentially expressed at least at one of the time points. The DESeq...Hi, I have RNA seq data for 7 time points with 3 replicates each, I would like to mark genes that are differentially expressed at least at one of the time points. The DESeq manual

DEseq2

updated 9.0 years ago • Abhishek Singh

the summary data seems wrong. At the end I also put the beta value matrix. R01C01 and R05C01 are replicates of SD-1. R02C01 and R06C01 are replicates of SD-1R and it goes like that. I don't know if duplicateCorrelation or avereps

limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19

updated 12 months ago • Melisa Tecik

limma. I have two treatments (treatment and mock) and three time points (1h, 9h and 24h) each with 3 replicates (total 18 libraries). I tried two models - one including the replicates (Model1) and another excluding the replicates...itself takes variance in the replicates in to account and doesn't need to include replicates in the model as in Model1. Accordance with that edgeR analysis..._mock', '…

limma RNAseq_Analysis model.matrix

updated 10.5 years ago • anver

Dear Gordon & list Why is it not possible to fit random block effect and technical replicates within array in the same linear model? Is it because - the statistical theory is not ready? - or - it is not implemented...S?rensen (HAG) Cc: bioconductor@stat.math.ethz.ch Emne: [BioC] random block effect and technical replicates within array at the same in linear model using Limma? > D…

Genetics limma Genetics limma

updated 20.5 years ago • Jakob Hedegaard

presently studying Limma package My data contains two groups and three time points with __NO__ replicates. One is an experimental group and the other is a control group I visualise to run the experimental group data individually...three time points between both the groups? Please can you recommend me a solution As there are no replicates, please suggest if i have to normalise the dat…

limma microarray agilent microarrays single channel

updated 9.0 years ago • ragavendrasamy.b

<div class="preformatted">Hi all, I am trying to use DiffBind to compare peaks called in control vs condition. I have 2 replicates for each and I've also called peaks using 2 different peak callers (to wi, MACS and QuEST). I've also prepared a sample data sheet that looks like this: SampleID Tissue Factor Condition Replicate Peak.caller bamReads bamControl Peaks control …

Genetics DiffBind Genetics DiffBind

updated 13.2 years ago • António Miguel de Jesus Domingues

<div class="preformatted">Dear Roberta, I have tried to answer your questions, but nothing that you mention is at all surprising or unexpected. >Date: Thu, 25 Oct 2007 16:04:39 +0200 >From: Roberta Sirovich <roberta.sirovich at="" unito.it=""> >Subject: [BioC] duplicateCorrelation dye-swap technical replicates >To: bioconductor at stat.math.ethz.ch &g…

limma limma

updated 18.1 years ago • Gordon Smyth

numbers, are in fact sharing the same unigene ID. I would like to find the gene records containing replicate unigene IDs and merge them into one record by averaging different expression values in the same condition. Could

Microarray Microarray

updated 20.7 years ago • zhihua li

for each cell type. I can do this by looking at the standard deviations of gene expressions between replicates. I am just wondering if there is any function in limma or other BioConductor package to do this. Thank you in advance

limma limma

updated 14.7 years ago • Wendy Qiao

Patient_3_untreated, So for each condition (tread V.S untreated), we have three biological replicates. I followed <4.4 RNA-Seq of oral carcinomas vs matched normal tissue> in edgeR Users Guide to analysis these...My questions are: 1.Could I say that, especially basing on the result of MDS-plot, the biological replicates are not consistent in my case, or the quality (fitness for …

RNASeq edgeR RNASeq edgeR

updated 12.4 years ago • sheng zhao

<div class="preformatted">Hi, I am trying to process sereral RNAseq using easyRNAseq package but I am facing an error I don't manage to fix. I use R version 3.0.2, and easyRNAseq version 1.8.2. I have 45 RNAseq with no replicates. I use this to call easyRNAseq, as described in the documentation: count.table <- easyRNASeq(filesDirectory= "/path...don't manage to fix. I use R vers…

RNASeq PROcess easyRNASeq RNASeq PROcess easyRNASeq

updated 12.0 years ago • Isabelle Stévant

sbcglobal.net" <noel0925@sbcglobal.net> Subject: Re: [BioC] Question regarding handling technical replicates for Affy arrays Date: Sun, 28 May 2006 06:23:30 -0700 (PDT) Size: 6059 Url: https://stat.ethz.ch/pipermail/bioconductor

updated 19.5 years ago • noel0925@sbcglobal.net

my infected time point with my mock time point. But here is the catch, I have pairs of biological replicates and then there were sets of technical replicates done off of those,so my question is how to address the biololgical...and technical replicates within the design and how to address viewing these differences within a contrast matrix . Would you set it up this...the dye swapped with those th…

updated 13.7 years ago • Richard Green

experiments with limma, but I am really not sure about the way to define tech and biol replicates. Any answer very welcome for me to know of my results are correct or not ... The experiment is as follow : I have...a mutant (mut) and a wild type (wt) strain x 2 biol. rep x 4 technical replicates So I have : mut1.1 ; mut1.2 ;  mut1.3 ;…

limma

updated 10.8 years ago • Florence Combes

it is a dye-swap >experiment. Presumably this means I don't have to treat the technical >replicates in any special way...? > >Mick That would be my interpretation, if everything else is correct. Technical variation

updated 20.2 years ago • Gordon Smyth

two color Agilent4x44 arrays) with limma,where Cy3 is normal and Cy5 is tumor.And all are biological replicates ,means all 10 arrays have been prepared from 10 different patients. there are two categories as nod negative and

Cancer Breast limma Cancer Breast limma

updated 15.4 years ago • neeraj rana

I want to pass a corrected model matrix to `DEseq` following the collapse of some technical replicates and I just wanted to make sure I am doing things in the correct order and grabbing the right data. First I created...object with a design including only 2 of the 3 elements of my design. Then I collapsed the technical replicates. Then filtered the collapsed counts, followed by the creation o…

deseq2 RNAseq model.matrix collapseTechnicalReplicates

updated 6.0 years ago • rbenel

a subset of genes that are significant in one of my differential expression analyses and then try to replicate those findings in another cohort of similar demographics (both are from gene expression using cord blood right

RNASeq

updated 3.1 years ago • S

Dear all: I need to understand multiple repeated testing for biological ChIP-seq replicates, to observe test variation in repeated multiple test. Can anyone tell me any related papers, journal review to...Dear all: I need to understand multiple repeated testing for biological ChIP-seq replicates, to observe test variation in repeated multiple test. Can anyone tell me any related papers, journal…

bioinformatics paper multiple treatments biologicalreplicates

updated 9.4 years ago • Jurat Shahidin

determining a list of DE genes for each time point of a series of experiments in which there are no replicates. (I am looking at the Spellman Yeast Cell Cycle data). On the one hand I am familiar with some methods such as that by

Yeast cycle Yeast cycle

updated 18.9 years ago • peter robinson

coefficients to fit, so estimation of dispersion is not possible. Treating samples as replicates was deprecated in v1.20 and no longer supported since v1.22. I can't figure out what the issue is, and would really

deseq2 rna-seq

updated 6.3 years ago • jpc41

with 2 types of stress: NaCl and CdCl2. I have pooled common reference and I have 3 biological replicates of treated plants. I also did dye swaps as technical replicate. This is my targets file: SlideNumber Name FileName...without normalization between arrays. Now I have the vector indicating biological and technical replicates. >biolrep=c(1,2,3,4,5,6,1,2,3,4,5,6) and create mode…

Normalization Clustering probe limma GLAD Normalization Clustering probe limma GLAD

updated 15.9 years ago • Michał Góralski

<div class="preformatted"> Dear all, I am working with limma package for the analysis of differential expression in agilend double color chips. My data come from a common reference experiment and the design matrix is the following: WT MU 1 0 -1 0 0 1 0 -1 1 0 -1 0 0 1 0 -1 Since rows 1 and 2 are technical dye-swap replicates (as rows 3 and 4, 5 and 6, 7 and 8), I am tryin…

limma limma

updated 18.1 years ago • Roberta Sirovich

Hi all, I need to reanalyse an RNA-seq experiment with 2 conditions and unfortunately no replicates. I probably don't have big changes in expression, 100-200 genes with logFC max 2-3. I'm planning to do the the following

rnaseq deseq2 tximport

updated 9.0 years ago • Endre Sebestyen

I am trying to find out the differentially expressed gene in a RNAseq experiment without replicate. The first R script is inspired by [__this post__](http://seqanswers.com/forums/showthread.php?t=31036) on seqanswer...I am trying to find out the differentially expressed gene in a RNAseq experiment without replicate. The first R script is inspired by [__this post__](http://seqanswers.com/forums/sh…

rnaseq deseq2

updated 9.8 years ago • prp291

human-pbmcs-10x-genomics.html#quality-control My question is: should the tSNE from biological replicates look somehow similar? I'm thinking in shape but also number of clusters. How can I be confident that cluster changes

scRNAseq SingleCellExperiment batchelor

updated 15 months ago • Jose Guillen

Chavez; bioconductor@r-project.org Subject: Re: [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS Hi Kelly, No, youshould not ignore the error message. I did not fully understand...mailto:bioconductor@r-project.org> Subject: [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS Hi Lukas, I have a …

Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS

updated 12.0 years ago • Vining, Kelly

array. > >I know how to fit blocks as random as explained in the Limma manual >(Technical replication I) >I know how to account for the replication within arrays. > > >Is it possible to fit random block effect and...technical replicates within >array at the same in linear model using Limma ? > >Thanks >Peter > &am…

limma limma

updated 20.4 years ago • Naomi Altman

to be a pretty basic set-up.  I have a panel of, say, 20 cell lines, c1, c2, …,c20, with two replicates for each cell line, so 40 samples total.  The cell lines can be divided into groups based on different phenotypic...15 in g3, c16-20 in g4.  And I’d like to compare, say, g1 with g2, which would be 10 samples (2 replicates each of 5 cell lines) in each group; then com…

deseq2 rnaseq differential gene expression

updated 8.1 years ago • Bob Thurman

I have a MAList and I want to exclude probes that show a standard deviation above 0.1 between the replicate values. The number of within-array replicates for each probe (ndups) is equal to 2 and the number of spots to step from

Genetics probe Genetics probe

updated 18.8 years ago • João Fadista

gt; Subject: Re: [BioC] edgeR > > Hi Mark, > > I have two samples "Y" and "S" (with no replicates), and following edgeR > manual on "what to do if you do not have replicates", I am getting the > following results below...d,design) > Warning message: > In estimateCommonDisp(d, design) : > There is no replication. Setting common dispe…

edgeR

updated 3.5 years ago • Gordon Smyth