Bioconductor Forum

is in bioinformatics, computational biology, genomics, data-mining, and related areas. Call for papers (Deadline Extended): BCBGC-10, USA, July 2010 The 2010 International Conference on Bioinformatics, Computational Biology...pools and on-site dining â all situated on 10 tropically landscaped acres. Here, guests can experience a full-service resort with discount hotel pricing in Orlando. We …

updated 15.7 years ago • John Edward

to perform differential expression analysis on some ATAC data. However, all I have is counts table for peaks (no beds or bams) and a meta table with the sample names and conditions they belong to. Is there a way to use diffbind...any benefit over simply using DESeq2 or edgeR? Thanks for the help in advance! #Fake example table peakname condition1r1 condition1r2 condition2r1 condition2r2 …

diffbind ATACseq ATAC counts differential analysis

updated 6.7 years ago • pgontarz

Because of technical limitations due to library prep time and index diversity, all Type 1 sequencing experiments were prepped and sequenced in one run, whereas Type 2 experiments were divided in 2 unequal batches. It is not possible...to prepare and sequence type 1 and type 2 together. Unfortunately, one of the batches (batch B) coincides with Patient 1, and it's not yet very clear to me wheth…

deseq2 rna-seq R linear model design matrix

updated 8.1 years ago • gdagstn

Are there tools implemented in Bioconductor that allow one to use technical replicates to batch correct. Meaning, if one has a group of samples that are repeated across known batches, are there tools that can use these...samples for batch correction

batch effect

updated 9.4 years ago • Juliet Hannah

gene was down or up regulated at different time points per breed and I want to have these info in a table. To be more specific : > PL<-read.csv("PietrLand.csv",header=TRUE) > dim(PL) [1] 6236 4 > class(PL) [1] "data.frame" > PL[1:4,] Gene.name...1 3 Ssc.14467.2.S1_a_at 1 1 1 4 Ssc.19413.1.A1_at 1 1 1 > q&am…

updated 19.2 years ago • daphne mouzaki RI

Hi, I am doing RNA-seq analysis using limma and edgeR, I have 48 samples and 2 batches. I built MDS plots (see below), and now my question is do I have a batch effect I need to correct for or not? My understanding...is if batches cluster together on MDS/PCA plot, it's an evidence that batch effects are present, am I right? <img alt="" src="https://imgur.com

limma rna-seq edger batches

updated 6.6 years ago • chipolino

In Bioconductor, it is required that the tarball size should be <= 4MB but my package's tarball size is 50MB. I checked the folders and found that the actual package is less than...1MB. Why is the size of the package's tarball high

R bioconductor

updated 8.5 years ago • Mohamad S. Hasan

model could be explained by sex svafit <- sva(geneExpression,mod) # we suspect some batch effect but we don't know from which variable it comes, so we use sva svaX<-model.matrix(~sex+svafit$sv) # we adjust with the...df.residual[1]) Code2 library(limma) mod <- model.matrix(~sex+batch) # we explain our model with sex and some b…

limma BatchEffect sva

updated 2.9 years ago • Lenny186

div class="preformatted">For normalization the batches of slides do not matter if you use the usual 2-color normalization methods, which normalize each slide separately...If you want to do multi-array normalization, you need to read all the arrays into a single batch. However, for analysis, you likely want to use some type of ANOVA. For this, it is more convenient to read in all of the arra…

Normalization Cancer Normalization Cancer

updated 21.8 years ago • Naomi Altman

I understood the examples of the Omixer pacakge. Because when I try to use a layout for multiple batch I was not able to make it work. Now that I made sure there are enough sites to allocate all the samples it tells me that the...with `filter()` input `..1`. #> ℹ Input `..1` is `mask == 0`. #> x Input `..1` must be of size 288 or 1, not size 237. Omixer_index <- omixerRand(s…

Omixer

updated 4.4 years ago • Lluís Revilla Sancho

Look for reference about paired analysis about microarray. I have a data set about a microarray experiment for same patients before and after treatment. Data Layout is show in belwo Table 1 Patient 1 Before surgery Patient...of interest, classify patients, and identify patients who respond to the surgery. Also, the sample size needed for further experiment is of interest. Typical …

Microarray Bayesian Microarray Bayesian

updated 21.7 years ago • Haiyan Wu

div class="preformatted">Dear friend, I'm trying to use your ComBat R script to eliminate batch effect when combine high-throughput gene expression data from different batches. However, there is an issue about the...skip=1,'clinicaldata.txt') Reading Sample Information File Reading Expression Data File Found 3 batches Found 66 covariate(s) Error in `[<-`(`*tmp*`, , i, value = c(NA, NA,…

updated 11.3 years ago • Shaowei Wu

gene 2 in lines 51-98.  <span style="line-height:1.6">My question is whether or not there is a batch correction function based on means or medians which I can apply prior to the various normalization functions in the...package, and what that would be called. For instance if one batch of 24 samples routinely has high Ct values compared to other batches I would like to adjust the Cp…

qPCR htqpcr

updated 8.9 years ago • bradley

Hi all, First post here, so apologies if I haven't explained anything clearly/followed standard guidelines. I'd like to create a summarized experiment object for downstream analysis of my count data from RNA seq analysis.  The way I do this is something like this...I haven't explained anything clearly/followed standard guidelines. I'd like to create a summarized experiment object for …

deseq2 summarizedexperiment rangedsummarizedexperiment rnaseq

updated 8.6 years ago • krc3004

div class="preformatted">Dear all, I would like to use Combat to correct for different batches (extraction date, hybridazation and amplification). In the description there is only on variable for batch, but i can...set more then one covariant, so should I use one for batch and the rest as covariants? Thanks you very much</div

updated 13.0 years ago • cirruswolke9@googlemail.com

0"> <tbody> <tr> <td>16-0384</td> </tr> </tbody> </table> </td> <td>RE_Co</td> <td>T0</td> <td>T0_RE_Co</td> </tr> <tr> <td> <table border="0" cellspacing="0"> <tbody> <tr> <td>16-0343</td> </tr> </tbody> </table> </td> <td>RE_Co...0"…

deseq2 interactions batch effect correction grouping variable

updated 7.2 years ago • mat.lesche

Hi,   I want to use edgeR for DEGs between two groups, but I find two batches in samples. So I intend to use Combat to adjust for differences between batches. I know edgeR is designed to

combat

updated 10.7 years ago • zhouxiuqing

Hi all, I wanted to know if it is possible to remove 3 batches using "limma". I have sequencing data with three possible batch effects: age, gender and working sets. As far as I understand...using limma's "removeBatchEffect" enables to remove only two batches categories by defining "batch" and "batch2" removeBatchEffect(x, batch=NULL, batch2=NULL, covariates=NULL, …

limma

updated 5.8 years ago • Matan G.

Hello! I am following the ___Aaron T Lun et al. 2016___ paper to analyze my brain scRNA-seq data, but I am blocked in the step of gene filtering. I have my data in an _sce object_ and I...Hello! I am following the ___Aaron T Lun et al. 2016___ paper to analyze my brain scRNA-seq data, but I am blocked in the step of gene filtering. I have my data in an _sce object_ and I have...ave.counts &gt…

size factor negative scran singlecellexperiment scater

updated 7.8 years ago • Marina V.V.

genome="hg38", tablename="refGene")_ _-----_ I am able to download the refGene table, but then receive the following error: _-----_ _Download the refGene table . . . OK_ _Download the refLink table . . . Error in normArgTable...value, x) : unknown table name 'refLink'_ _-----_ Upon looking on the hg38 genome browser it appears that the refLink table is still connected to the...refGene tabl…

annotation

updated 9.2 years ago • cmarcone

I am performing a differential expression analysis between treated and untreated cell lines using DESeq2. The samples were sequenced in two different batches, however, there is a perfect confounding of the conditions and the batches. All controlled samples are in one batch and all treated samples are in the second one. The perfect confounding does not allow to remove batches or even account for t…

DESeq2 DifferentialExpression

updated 4.7 years ago • rina

I have RNA-Seq data from two batches and know there is significant batch effect in the data.And I just want to get the normalized data without batch effect...row.names = FALSE) > ddsHTSeq1<- DESeqDataSetFromMatrix(counts.spikein, colData, design =~batch+condition) > dds1<-DESeq(ddsHTSeq1,full=~ batch + condition, reduced=~batch, test="LRT") estimating size factors …

deseq2

updated 6.7 years ago • Nicola

variables is affecting my results. For example, I am wondering if it makes sense to include "batch" in my design. Before doing any analysis, I made PCA plots from my data, and the samples do not seem to cluster by batch. If I...run DESeq to compare across disease state without controlling for batch in my design and then generate a heatmap with hierarchical clustering, the samples from the sam…

DESeq2

updated 4.8 years ago • lransom

Hi, after an RNASeq analysis using Limma I obtained a table full of genes by using the topTable() function. So I have a csv, comma separated, formed by GENEID(ensemble), ENTREZID, SYMBOL...there a way to search the most significant genes associated to a specific disease mentioned in some papers? Because for e.g. the top 5 genes are not mentioned in any paper to be related to some diseases. The ta…

GeneExpression RNASeqR limma

updated 5.0 years ago • Will

Hello, I have a time course RNAseq experiment with 2 different genotypes and 2 times (0h and 2h), there are 3 replicates each time I am looking for a way to output...2h VS 0h in condition B). I don't know if it is right to directly compare the FoldChange from both tables. Also, some genes do not have the same expression level at 0h. I was more thinking of making a new analysis using a desi…

DESeq2 RNASeqData DifferentialExpression

updated 2.9 years ago • Julie

Can I use ComBatSeq function instead of ComBat to adjust for batch effect in microarray data? I know the description of ComBatSeq is for RNAseq but when I tried both functions, ComBatSeq...was more efficient in removing batch effect compared to ComBat. ![ComBat-Seq][1] ![ComBat][2] [1]: /media/images/40a00310-c2ca-424d-9268-fc58f939 [2]: /media/images/9bb0aca6

BatchEffect sva MicroarrayData

updated 7 months ago • Shaimaa Gamal

and there are two sequencing platforms used, illuminaHiseq and IlluminaGA. Is there a way to remove batch effects in DESeq2 package prior to differential expression or does the GLM remove it automatically (which i dont hink

deseq2 batch

updated 6.7 years ago • sherajilir

differential gene expression between healthy and KO mice. I know that there is a very strong batch effect that I have to adjust for. I read both on this forum and on _Biostar_ that it is generally recommended to include...the batch effect in the limma model instead of using for example _Combat_seq_ to adjust for the batch effect. I wanted to make sure...that limma can appropriately control for…

BatchEffect limma sva DifferentialExpression

updated 3.8 years ago • nhaus

div class="preformatted"> How do I generate a simple table similar to the following link in R http://www.fedstats.gov/policy/publications/wp1fig1_text.html Table 1 Poverty

updated 15.5 years ago • David Lyon

class="preformatted">Dear list, I got 12 Affymetrix arrays for 4 RNA samples, 3 replicates(from 3 batches individually) for each sample. I want to look at the differential expression between these samples. While after clustering...we found obvious batch effect within the data, so we decided to add the batch effect into the linear model. I set up the design matrix as followings...is any proble…

Clustering Clustering

updated 16.3 years ago • Yuan Hao

div class="preformatted">Dear All, Is there an equivalent of the table function for a GenomicRanges object? Best, Vedran -- Vedran Franke Bioinformatics Group, Department of Molecular Biology

updated 13.0 years ago • Vedran Franke

Hi bioC community, Until now I used comBat to remove the batch effects present on my datasets. After reading the article "Methods that remove batch effects while retaining group...content/early/2015/08/31/biostatistics.kxv027.full.pdf>, I decided to block for batch effect in limma in the case where the groups are distributed between the batches in an unbalanced manner. But I am wondering...…

batch effect combat limma block

updated 10.2 years ago • eleonoregravier

As far as I understand, The process by which DESeq2 models a batch effect is close to : Subtracting the arithmetic mean of the batches' expression values from the genes, on a per-gene basis...Is it possible in DESeq2 instead of modelling only an additive batch effect, to model a multiplicative one as well? For example, divide the expression levels per gene by the batch-specific...geometric mean?…

deseq2 batch-effects ComBat

updated 6.2 years ago • Sam

Hi all, I have a problem in figuring out how to include the batch effects in the design formula of DESeq. In particular I have to test the effect of one condition (Low protein diet vs Control...liver samples (24 for each condition). The problem is that I sequenced the samples in two separate batches (always keeping Treated vs Control in each batch) and different sequencer. So I have 2 big …

DESeq2 BatchEffect RNASeq

updated 3.1 years ago • Flavio

the same gene universe for 2 different gene enriched sets, there are different number of GO term sizes for the same GO term:   An example Gene set enr: 1480 <table border="1"> <tbody> <tr> <th>GOBPID</th> <th>Pvalue</th> <th>OddsRatio</th> <th...ExpCount</th> <th>Count</th> <th>Size</th> <th>…

gostats hypergeometric test

updated 8.8 years ago • tlaguna

Hi, I am new to batch effect correction and apologize if this is a naive question. My goal is to determine how similar my cell line is to the...database. I have the RNA-seq profiles for both samples, but they are obviously from two different batches, and any possible biological differences are confounded with batch. A colleague of mine suggested that I can still...batch effect correct to check …

sva BiologicalQuestion

updated 9 months ago • bbao

Dear Users, We have a CyTOF experiment containing 91 samples distributed in 10 batches, with one anchor for normalization in each of these batches. However...Dear Users, We have a CyTOF experiment containing 91 samples distributed in 10 batches, with one anchor for normalization in each of these batches. However, I can't figure out how to make it work: I would like to tell the fu…

Cydar normalization normalizeBatch

updated 6.7 years ago • Florent

ALL, in conjuction with one previous post about the correct implementation of ComBat() function for batch effect correction, \[<span style="line-height:1.6">__https://support.bioconductor.org/p/77726/__\]</span> i would like to ask...dl=0__ So, i understand that the black line represents the kernel estimate  of the empirical batch effect density, and the red the parametric…

ComBat diagnostic plot batch effect affymetrix microarrays sva

updated 9.8 years ago • svlachavas

Hi,  I have a question concerning insertion size when using MEDIPS. When setting paired = TRUE in MEDIPS, you will get a mean insertion size as well as standard deviation...Mean insertion size: 204.4319 nt SD of the insertion size: 57.93392 nt Max insertion size: 602 nt Min insertion size: 49 nt Does the insertion...size include the reads or is it the number of nucleotides be…

medips R medip-seq pair-end reads

updated 9.0 years ago • stb

div class="preformatted">What anova table do you want exactly? lmFit() fits a linear model for each probe. Do you want 55,000 anova tables if there are 55,000 probes? That...34:15 -0500 > From: Jianping Jin <jjin at="" email.unc.edu=""> > Subject: [BioC] limma anova table? > To: BioConductor_list <bioconductor at="" stat.math.ethz.ch=""> > Message-ID:…

probe limma probe limma

updated 19.8 years ago • Gordon Smyth

in itself a simple form of spatial normalization (as well as intensity-based normalization). In my experience, print-tip-loess does most of what spatial normalization would have done. But, as you say, if you really do want to...formal 2D normalization you'll have to do it outside of limma. >I am also running a Genechip experiment, with four time points and three >treatments (A,B an…

Microarray Normalization limma Microarray Normalization limma

updated 22.3 years ago • Gordon Smyth

Hi, I would like to use _sva _package to adjust for the effects of batch on two independent datasets. Ideally, one dataset should be the training set, while the second one is for prediction. My...Hi, I would like to use _sva _package to adjust for the effects of batch on two independent datasets. Ideally, one dataset should be the training set, while the second one is for prediction. My underst…

sva combat gene expression batch effect rnaseq

updated 10.2 years ago • Farshad Farshidfar

Hello, usually I load the condition table from a table in order to have a data frame with a column called condition that I put in the design formula: <pre> dds = DESeqDataSetFromTximport

deseq2

updated 8.5 years ago • ribioinfo

keeping into account only the stage when creating the DE object like this (an example of my design table is at the end of the post): <pre> (design=~stage)</pre> Using this approach and following the guidelines described in the tutorial...Another alternate approach I thought was to use sva or other packages to remove the "timepoints batch effect" in each stage, however I still haven…

drosophila melanogaster multiple time points deseq2 results development

updated 8.7 years ago • wariobrega

a user visible change to the empirical Bayes procedure used in the limma package. I have changed the hyperparameter estimation to make it less sensitive to sample standard deviations which are zero to machine precision...The only exception is for data sets which have many exactly zero standard deviations, which may experience somewhat less smoothing than at present. The data sets for which the c…

limma limma

updated 20.1 years ago • Gordon Smyth

something extremely stupid here. I have 76 plates(in 96 well format) in dulipate, and first 3 batch each has 20 plates within a batch(with duplicate, which means 40 plates total for each batch). my code to define the batch...to the description of the package I need to define a array with dimension of (96*76,2,1) to feed to "batch" function) "DL" is my cellHTS object; ind=c(rep(1:3,each=96*20),…

cellHTS cellHTS2 cellHTS cellHTS2

updated 17.1 years ago • yan zhou

differential transcript level expression analysis and I have 3 groups that were sequenced in 5 batches I am trying to run swish on the data to get differentially expressed transcripts however my batch distribution is...8 8 1 > Batch4 0 11 12 > Batch5 8 8 8 As some batches are 0 or 1 when I run the following command between two groups I g…

Differentialtranscripts fishpond swish

updated 2.3 years ago • priyanka

if anyone knew where the python module is to carry out pathway analysis using the methods in the paper by Kim and Volsky (2005) in their paper "PAGE: Parametric Analysis of Gene Set Enrichment paper"? It is not clear if they...produced a python module from the paper and if they did i have not been able to find it! Any help would be great to point me in the right direction Thanks Danie…

GSEA PAGE microarray differential gene expression pathway analysis

updated 8.7 years ago • danielle.newby

<div class="preformatted">2009 World Congress on Computer Science and Information Engineering (CSIE 2009) March 31 - April 2, 2009 Los Angeles/Anaheim, USA http://world-research-institutes.org/conferences/CSIE/2009 CALL FOR PAPERS, INVITED SESSIONS & EXPO The Los Angeles/Anaheim area is known for its many renowned attractions, such as Disneyland, Universal Studios and the Hollyw…

updated 17.2 years ago • Hongping Wu

to find differentially methylated CpG sites. Both of the datasets are from EPIC array, but different batch(batch 0 and batch 1). I've already tried to correct the batch effect using [Harman batch correction][1] ```r shifted_betas &lt...cex.main=0.7) shifted_ms methHarman <- harman(shifted_ms, expt=targets_pr$Sample_Group, batch=targets_pr$batch, limit=…

BatchEffect limma methylationArrayAnalysis

updated 2.0 years ago • kyj2226

So, I've had the BHC package working for a time course experiment before. I'm trying to use the multinomial option instead of the timecourse one and it's breaking, spectacularly...So, I've had the BHC package working for a time course experiment before. I'm trying to use the multinomial option instead of the timecourse one and it's breaking, spectacularly. The basic use case in the documentation …

bhc

updated 10.6 years ago • b.curran

Hi: I am experimenting preprocessed Affymetrix microarrays expression data matrix (Affymetrix probe-sets in rows (32830 probesets...in columns (735 samples)) for my downstream analysis. However, I have `pheno` metadata for the experiment observations. **data that I used**: > dim(eset_HTA20) [1] 32830 735 > eset_HTA20[1:3, 1:3] Tarca_001_P1A01 Tar…

limma microarray error

updated 6.4 years ago • Jurat Shahidin

CS, ECE or related field. Alternative degree fields will be considered if accompanied by equivalent experience as it relates to current NCSA projects. 1-3 years of experience in biological computing, such as genomics, transcriptomics...phylogeny, molecular modeling, computer simulation of biological processes, etc. Experience documenting projects, research effort and codes. Preferred Requ…

supercomputing bioinformatics VariantCalling healthcare Agriculture

updated 4.0 years ago • Jenny Drnevich

Dear all, I am working with a RNASeq data from an Arabidopsis experiment. The plants have been subjected to nitric oxide treatment for 3 hours and for 8 hours. I would like to find differentialy...the section "3.3.3 Treatment effects over all times" of edgeR user guide. The design of the experiment is 3 biological replicates for each of the 3 samples: <table border="1" cellpadding="1" cells…

DGE rnaseq RNA edger

updated 8.6 years ago • Pietro

Hello, I'm struggling with batch correction for RNA-seq data in DESeq2. For example, my colData looks like this (10 samples, 6 controls+4 treatment, belong...to 2 batches): samples condition batch 100 PH7 1 101 PH7 1 103 PH7 1 63 PH7 1 64 ctr 1 74 ctr 1 …

deseq2 batch effect

updated 6.4 years ago • Rimma

packages* What should I do to load the airway package sessionInfo( ) *R version 4.1.2 (2021-11-01) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.1 Matrix products: default LAPACK: /Library

airway

updated 3.9 years ago • j.jacob1

colnames(pData(eset_NONE)); table(pData(eset_NONE)[,"**Study**"]); table(pData(eset_NONE)[,"**Disease**"…

affy insilicomerging

updated 6.7 years ago • pratikshasharma47

Hi I am almost finished my package and the paper is nearly done too. Which order do I submit these in? Do I wait for it to be accepted by the bioconductor then submit to journal

bioconductor

updated 8.5 years ago • chris86

very well if your log-data are fairly normally distributed (within each gene) and if your sample size is relatively large (say ~15-30). If you have a small sample size or if your data (within each gene) are not normally distributed...gt; Content-Type: text/plain; charset="iso-8859-1" > > I'm trying to analyze an RNA-seq experiment where the PCA plot shows better > clustering …

GO Clustering edgeR GO Clustering edgeR

updated 12.5 years ago • W. Evan Johnson

it successfully for a qPCR array with 96 genes. I was wondering if someone knows about a couple of papers where limma is used to assess DEGs in a qPCR array and not on another microarray platform or RNA seq. I know it's perfectly

limma

updated 7.4 years ago • Daniel Moreno