Bioconductor Forum

table border="0" cellpadding="0" cellspacing="0" style="width:100.0%"> <tbody> <tr> <td> <p><strong>SUMMARY OF POSITION:</strong></p> </td> </tr> <tr> <td> <table...projects, and work on independent projects that are solely computational.</p> </td> </tr> </tbody> </table> </td> </tr> …

Bioinformatician Job

updated 11.1 years ago • Julie Zhu

I have a paired test situation, (with and without treatment) on 8 samples. The experiment is (targets.txt): <pre> files Subject Treatment r1.txt 1 NO r2.txt 1 TREAT r3.txt 2 NO r4.txt 2 TREAT r5.txt 3 NO r6.txt...for r1 an r2) were sequenced in another run (different time). I wonder how to remove the \*\*batch …

edger design and contrast matrix

updated 11.0 years ago • Son Pham

a few questions about use cases for the pigengene package. 1. For our dataset, I provided both a training dataset and a test dataset, and the one.step.pigengene function did not appear to take the test data into account...and testLabels). My question is, does the test data have to be same dimension or similar sample size as the training set in order for the function to provide the accuracy of tr…

Pigengene

updated 2.1 years ago • kjngo

__Johnson and Li. 2007, Adjusting batch effects in microarray expression data using empirical Bayes methods__, is the paper for the comBat package, and I have...across all other genes__, possibly protecting their inference from artifacts in the data. In this paper, we extend the EB methods to the problem of adjusting for batch effects in microarray data.  Could anyone please explain

ComBat microarray batch effects

updated 8.4 years ago • DataFanatic

data sets on different stress conditions (say A, B and C). The authors who actually performed these experiments performed cluster analysis using FPKM and normalized across all the stress conditions. In the paper, they mentioned...nbsp; count\_table<-read.table("all\_expr.txt", header=T, row.names=1, sep="\\t")     batch<-factor(c(rep("stress\_A",6), rep("stress\_B…

deseq2

updated 7.1 years ago • sancharisircar24

My group is working on method development, and I have an experiment where the samples are 0/100, 20/80, 40/60 60/40,80/20,100/0 mixes of two different tissues. I wanted to use DESeq and treat...My group is working on method development, and I have an experiment where the samples are 0/100, 20/80, 40/60 60/40,80/20,100/0 mixes of two different tissues. I wanted to use DESeq and treat this like a…

deseq2

updated 5.2 years ago • swbarnes2

y,design) fit<-glmQLFit(y,design) Normalized_counts<-cpm(y) Now I added another batch of data for 6hr and I want to include the batch effect in the analysis. After reading similar posts, I think one possible...way would be to add a new **'batch**' column to target file and address that in the design matrix. Like, Sample Geno Time Treatment Batch Sampl1 KK 2h…

edgeR BatchEffect RNASeq

updated 5.0 years ago • anikng

39(13 samples with 3 replicates) samples. I would like to do a PCA analysis. Apparently, there is batch effect in data. I would like to remove these batch effects and see how my samples would cluster after removing batches...I am following the instruction from [this paper][1]. [1]: https://f1000research.com/articles/4-1070 here is my experiment design. ``` coldata[,-c(1,2,7)] B…

sva deseq2 batch effect PCA heatmap

updated 6.5 years ago • bioyas

via machine learning algorithms in R, a 39-gene signature I have already developed in an independent training set, which could discriminate colorectal cancer from control samples. In my latest step, I would like to implement...ComBat to correct for batch effect regarding the different dataset-study, and then apply my classifier. In detail, __I merged the 4 different datasets...would like to use f…

affymetrix microarrays sva combat sva batch effect plotMDS

updated 9.3 years ago • svlachavas

of control replicates was sequenced earlier. Thus only this control replicate belongs to a different batch from all other samples. As suggested in the vignette I added batch in my design like `` ~batch+condition ``. However very few...genes remain significant after doing this as compared to when do not add batch to design. Is it recommended to add batch to design in such an experiment? Is there…

deseq2 rna-seq

updated 7.3 years ago • bn3301

18:58 To "'bioconductor@stat.math.ethz.ch'" <bioconductor@stat.math.ethz.ch> cc Subject [BioC] batch info for cellHTS2 Hello, I'm a NIH scientists that is doing a HTS experiment and I'm using your Cell HTS2 software to analyze...our results. I'm doing two different experiments with 2 repeats for each of them. I want to combine the results and thought to try the batch function. Currently,…

Normalization cellHTS2 Normalization cellHTS2

updated 16.1 years ago • florian.hahne@novartis.com

Hi, I have a question regarding large differences in library size amongst my samples. These samples are from invivo animal infection experiment and some samples had to be resequenced...to get enough reads. I do not have a case/infected and control/uninfected scenario in this experiment, they are just all infected samples. The range of library size in my experiment is 100,000 to 81 million. I g…

PCA DESeq2 Normalization librarysize

updated 5.1 years ago • pkachroo

I have samples from 1 experiment (experiment A) distributed in 2 sequencing runs. This experiment consists of 3 biological replicates, and the first...function. Moreover, the 2nd sequencing run contains also samples from a different experiment (experiment B). Now I want to analyse the experiment A using DESeq2, correcting for the batch effect with design=~batch...It’s simplified. In real…

DESeq2

updated 3.9 years ago • turtle012

technical replicates to be small and non-systematic in the PCA (B). Now I had the event of a batch effect between technical replicates (A). The experiment was design with 6x biological replicates (6 different samples...between groups. As discussed in https://support.bioconductor.org/p/85536/. Now for the case of a batch effect between technical replicates (A), it gets a bit ambiguous for m…

rnaseq deseq2 differential expression batch effect replicates

updated 6.2 years ago • Nik dAK

div class="preformatted">Hi BioC List, I'm working with an affymetrix data set where the batches are completely confounded with the factor of interest for one contrast, treatment time. From my understanding I...we do have the original tissue samples and the option to re- extract/reprocess some samples in a new batch. Due to the study size, rerunning all samples with a proper randomized desi…

updated 11.4 years ago • Ty Thomson

conditions: HLT and TUM These two conditions derives from aggregating data from 3 different experiments (which use different platforms also). I want to compare HLT vs TUM minimizing the batch effect, thus I implemented...in the design matrix both the condition and the experiment info: g = c(rep('HLT',9),rep('TUM',9)) conditions = factor(g, levels = c('HLT','TUM')) b = rep(c(r…

batch effect limma batch effect correction

updated 6.8 years ago • ginlucks

<div class="preformatted">Hi - There are a number of people in our branch and potentially at NIH interested in using bioconductor for microarray analysis. I was wondering if we could set up a training session which introduced bioconductor briefly and then provided a hand-on analysis of microarray data? Could you...NIH interested in using bioconductor for microarray analysis. I was wonde…

Microarray Cancer Microarray Cancer

updated 22.6 years ago • Joshi, Nina NIH/NCI

The deadline to nominate a qualified candidate is May 31, 2021! Our awardees will be selected, each having contributed to the project in an outstanding way based on one or more of selection

Bioconductor Bioc2021 Recognition Awards

updated 4.5 years ago • shepherl

Due to a limited budget, I wasn't able to conduct my experiment in one batch. Instead, I ran the experiment 8 times, twice for each genotype, with each batch containing both a control...me from including it in the end. I believe the error stemmed from a lack of replication within each batch. Is it possible to account for a batch effect using this design? ![enter image description here][1] …

DESeq2

updated 3.5 years ago • Stephan

I have a quick question concerning the removal of the batch effect using removeBatchEffect()…   I have RNA-seq data and i have three batches. I normalize using spike in RNA and i...I have a quick question concerning the removal of the batch effect using removeBatchEffect()…   I have RNA-seq data and i have three batches. I normalize using spike in RNA and i estimate size fac…

limma rnaseq batch effect pearsoncorrelation

updated 9.8 years ago • elpsakkas

div class="preformatted">Dear BioCs, I need to download a complete set of experiments from GEO, with some hundred of single experiments. To import directly in R I want to use AnnBuilder, but I can only...download one array per time. How can I download them in batch mode throught AnnBuilder? Thanks in advance Claudio Isella. </div

updated 19.7 years ago • claudio.is@libero.it

div class="preformatted">Hello, I assume that "Size" column in the table generated by summary() of "GOHyperGResult" object produced by hyperGTest() function from "GOstats" package...is the total size of a given GO category. In this regard I am puzzled why values in this field are slightly different for the same GO categories

GO Category GO Category

updated 16.8 years ago • Sergei Manakov

div class="preformatted">Hi Everyone. Is there an organization that can be hired to train our scientists in Bioconductor? We would like to sponsor a training in house. Is there a training or course on Bioconductor...in the Boston Area soon (before Dec)? If not in the Boston area, is there a training or course on Bioconductor elsewhere soon? Thanks for your help. Best Regards, Eric Grund …

updated 21.1 years ago • Eric.Grund@serono.com

I'm going to be using frmatools to generate experiment-specific fRMA vectors from a set of training data, and these vectors will be used to normalize that training data...them in this way cause problems for the analysis? Second, what is the proper way to define a batch? Is there one correct way? Specifically, since my samples are all the same tissue, should I include the sample condition...in my…

frma frmatools

updated 10.8 years ago • Ryan C. Thompson

dataset (different hospitals, different days, etc.) we have to take into account the so-called batch effect. I have been practising with some useful tool such as SVA package but someone else like to cope with this issue...dataset and designing a matrix. I have always wondered why doing a t-test might control the batch effect, someone more expert than myself said that this is not so robust. It…

deseq2 batch sva t-test design matrix

updated 6.6 years ago • Mozart

phenotypes to the same control while also blocking for `subject_ID` that are repeatedly measured in batch 1 and batch2. **Experimental design** ```r # print meta data > pb.colData condition subject_ID_unique subject_ID batch 01501_b2...is the identifier for every sample. `batch` is a factor I wish to regress out. `subject_ID_unique` is `subject_ID` plus `batch` to make a …

covariancematrix limma

updated 17 months ago • jiachengd

I am currently trying to analyze a set of expression experiments from different tissues. Some of the expression profiles originate from knockout experiments, for which we expect...to cause trans-differentiation. The experiments suffer from strong batch affects which are unknown, but fortunately, not perfectly confounded with biological...variables of interest. I have tried using sva to find th…

sva svaseq batch effect batch effects batch effect correction

updated 8.3 years ago • vedran.franke

Targets Time Treatment Batch F21.CEL I18 18 I 3 F22.CEL I18 18 I 3 F25.CEL N18 18 N 3 F26.CEL N18 18 N 3 F23.CEL R18 18 R 3 F24.CEL R18 18 R 3 F19.CEL S18 18...4 F54.CEL S28 28 S 5 F55.CEL S28 28 S 5 The replicates in this experiment are biological replicates not t…

updated 19.9 years ago • Ron Ophir

Hi there, I'm hoping to get some help with the design table for my analysis, I continue to get the model.matrix error when I put it into DESeq2 and I'm not sure how to resolve this...Hi there, I'm hoping to get some help with the design table for my analysis, I continue to get the model.matrix error when I put it into DESeq2 and I'm not sure how to resolve this. Below...I have included an examp…

ExperimentalDesign RNASeq replicates DESeq2

updated 3.6 years ago • Beth_b

Hi, I wonder if I can regress out batch effects from my single-cell data using following strategy. Though the tutorial suggested using limma to remove batch...countData = sub_count_matrix, colData = cell_metadata, design = ~ Batch + Condition ) # size factor was pre-estimated using scran sizeFactors(dds) <- size_factors dds <- DESeq( …

DESeq2

updated 20 months ago • kys91240

Hello, I am running DESeq2 with this metadata table - | Condition | Time | Batch | |-----------|------|-------| | Control | 0h | 1 | | Control | 12h | 1 | | Control | 24h | 1 | | Control | 0h | 2 | | Control | 12h | 2 | | Control | 24h | 2 | | Control | 0h | 3 | | Control...I would like to model interactions between condition and time, but I …

DESeq2

updated 12 months ago • bhandary.8590

Dear all, I have a bulk-rna dataset which I have analyzed by DESEQ2 and I have batch corrected it using limma package and removeBatchEffect() function. I would like to calculate the FPM value for expression...deseq2. I know it will use the raw data to calculate these value. I have created a heatmap from my batch corrected data for some genew and I wanted to also plot the fpm value for these gen…

deseq2 limma

updated 6.3 years ago • Emir

Dear all, I have the experiment with the design like this: [design][1] ---------- When I used the DESeq2, I used the code: dds <- DESeqDataSetFromMatrix(countData...countdata, colData=coldata, design=~condition + batch) to remove the batch effect. However, I found the error: the model matrix is not full rank. I have read many threads about removing...batch effects as well as model …

deseq2

updated 5.7 years ago • luongthang1908

the following condition (where batches **I, II and III** are different days of the year): factor_1 batch sample1 neutrophils_cancer_type1 I sample2 neutrophils_cancer_type1...as input for DESeq2). So, once you've generated your SampleTable, if your samples come from the same batch I know that you are ready to go with …

deseq2 batch effect batch

updated 6.5 years ago • Mozart

Hi, I have single cells data from  two different experiments and I would like to remove the batch effects from the data in order to cluster correctly the cells. I would like...to try to see what are the differences removing the batch effects due to housekeeping genes and also to try to remove the batch effects that are not specifically due to the housekeeping

RUV single cell batch effect

updated 8.7 years ago • ribioinfo

<div class="preformatted">Microarray & high throughput sequencing data analysis with Bioconductor This course consists of lectures and hands-on labs. Days 1 to 4 will focus on all aspects of the data analysis of microarray experiments including preprocessing, quality assessment, differential expression, machine learning, etc. Additional talks will address genotyping and image analy…

Sequencing Microarray Annotation Normalization Preprocessing probe Sequencing Microarray

updated 16.1 years ago • Wolfgang Huber

https://forms.gle/d9PyAjAw62yVKxjL8) to nominate someone. The deadline for nominations is May 31, 2021

Awards Recognition Bioconductor Bioc2021

updated 4.7 years ago • shepherl

specific question about the less "erroneous" procedure regarding the implementation of ComBat and batch effect correction in microarray datasets. In detail, my goal is <span style="background-color:rgba(252, 251, 248, 0.901961...test a 39 gene signature that i have aqcuired, through a feature selection procedure in R-based on a training microarray dataset-, in 5 independent datasets, …

microarray batcheffectcorrection affymetrix microarrays ComBat sva

updated 9.4 years ago • svlachavas

Hello, I'm trying to remove batch effect from a dataset that include three experimental conditions (C_25,C_50,C_CTRL) and three batches (1,2,4). I prepared...a table with all these information (targets) and then I tried to create a design matrix using ~0+group+batch in my model formula...package. The code and the outputs are the following: ```{r} group <- factor(targets$CONDITION) batch …

edgeR model.matrix BatchEffect

updated 2.8 years ago • greta

any reasons why using ComBat with RNA-seq data is not legit? Here is what Evan had to say: "For batch effects, if the sample sizes are large, say around 10 per batch or more, ComBat and SVA will work fine regardless of whether...they are on count data or not. For cases with 50-100 per batch, ComBat and SVA will work extremely well and will be somewhat optimal. Basically this is due to the Centr…

sva sva

updated 12.3 years ago • Christopher Conley

div class="preformatted">I'm trying to analyze an RNA-seq experiment where the PCA plot shows better clustering by the day the experiment was done rather than treatment type. Using...expressed genes resulted in less than 5 genes with an FDR under 5%. Creating a GLM model to remove batch effects for day of experiment as stated in the edgeR manual resulted in 42 genes with an FDR less than 5%. A…

GO edgeR GO edgeR

updated 12.5 years ago • David O'Brien

Dear All, I have a list with 9 single cell experiment (SCE) objects which I want to integrate using **batchelor::fastMNN**. The experiment design is: 3 donors gave their blood...Dear All, I have a list with 9 single cell experiment (SCE) objects which I want to integrate using **batchelor::fastMNN**. The experiment design is: 3 donors gave their blood in 3 different times and their blood was st…

fastMNN SingleCellData BatchEffect batchelor

updated 13 months ago • José

I’m trying to recreate the results from this Alzheimer’s paper for further analysis (https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0355-3) Specifically...the supplementary table 4A reports genes significantly differentially expressed between brain donors that have Alzheimer’s vs. those that...is the microarray expression data, called alzheimers ![Alzheimer's expression …

limma edger linear regression microarray differential gene expression

updated 6.8 years ago • ravelarvargas

patients. Most of the Controls were processed in batch#2. To batch-correct, two technical replicates of lesional samples and two technical replicates of non-lesional samples...were also included in batch #2. All samples have **Patient ID** and **Sample ID**, like so: | Sample ID | Sample Type | Patient ID | Batch | |----------------|-------------------|----------------------|---------| |S1 |…

RUVSeq sva limma

updated 2.2 years ago • Jonathan

Hi, Library size is a source of unwanted variation in my data (dataset of healthy vs disease samples) because I can see in the pca plot that...samples are separated to some degree by library size. Can sva remove the effect that library size has on my data or is another package better suited for this? To be clear: I'm not...trying to remove batch effects. Thanks

sva

updated 3.4 years ago • Jasmin

manual 'differential analysis of sequence read count'. I have found some inconsistencies in library size preparation. In the manual, the library sizes for each sample should be the average of the total read counts for the methylated...Methylation=="Un"] ``` Could You explain to me the difference between both approaches? In other papers, there are also two different approaches. Regards

RRBSdata edgeR methylationArrayAnalysis

updated 2.4 years ago • Krzysztof

design matrix produces a 'Model matrix not full rank' error. What do you think I should do?   \# Experiment: We have three variables of interest in our analysis: Timepoint (A and B), Sex (M or F), and Condition (cond1 or cond2).&nbsp...B. Each possible Timepoint x Sex x Condition has its own unique samples. In our first sequencing batch, we collected samples for each possible com…

deseq2

updated 7.1 years ago • kmuench

Hi all, I have a question concerning microarray normalization followed by batch correction. I have a single experiment with patient data on two time points and I would like to compute the differential...expression between both time points. The samples were analysed in 2 batches. Batch 1 contains 32  samples (16 on time point 1 corresponding with 16 on time point 2),…

microarray normalization sva

updated 10.0 years ago • grla

with this. `` baseMean : It is defines as ``__average of the normalized count values, dividing by size factors, taken over all samples in the _DESeqDataSet___ After this step of the analysis, <pre> ddsMat <- DESeqDataSetFromMatrix...pre> I ran <pre> ddsMat <- DESeq(ddsMat)</pre> In the above calculation I see __estimating size factors__ I want to know …

r deseq2

updated 9.7 years ago • gv

TreatedB vs Untreated; TreatedA vs TreatedB). The final format for each of these tables was as follows: Gene Treated1(Replicate1) Treated2(Replicate 2) Untreated1(Replicate1) Untreated2(Replicate2) tag_id...must first normalize the expression values of each treatment by dividing each column with it's own size factor... however, when I want to estimate the size factors for any of my th…

DESeq DESeq

updated 13.3 years ago • Andres Eduardo Rodriguez Cubillos

due to the sample number limitation of the sequencing machine. So they have to divide into 2 batches for sequencing. Following sequencing, I used Tophat2-featureCounts-DEseq2 pipeline to analyze them.  My question...result into one file as the input for DEseq2? Is it OK that I run the pipeline for each batch of samples, generate the DE results (Condition vs control) and then compare the …

deseq2 featurecounts rnaseq

updated 9.4 years ago • EJ

I am wondering whether there is a straightforward method for updating a training set created by `DECIPHER::LearnTaxa`. I have new sequences that I'd like to include in the training set but as far as I can...I am wondering whether there is a straightforward method for updating a training set created by `DECIPHER::LearnTaxa`. I have new sequences that I'd like to include in the training set but as …

DECIPHER

updated 3.0 years ago • Connor

the gene expression. The thing is that samples from the 9 pts with Drug A were processed in one batch, and samples from the 9 pts with Drug B were a different batch. I am lacking experience in analysis, but I am concerned that...application of a batch correction method such as CombatSeq would potentially treat true treatment effects as batch effects and flatten...detectable differences. Would …

BatchEffect RNASeq

updated 2.8 years ago • chf

Course: Proteomics Using R/Bioconductor ONLINE, 15-17 March 2021 Instructor: Dr. Laurent Gatto (de Duve Institute, UCLouvain, Belgium) Course website: https://www.physalia-courses.org...Course: Proteomics Using R/Bioconductor ONLINE, 15-17 March 2021 Instructor: Dr. Laurent Gatto (de Duve Institute, UCLouvain, Belgium) Course website: https://www.physalia-courses.org/courses...i…

ProteomicsWorkflow proteomics Proteome

updated 5.0 years ago • info

differential gene expression analysis with edgeR. I have four conditions T1, T2, T3 and T4 and two batches. I am running the following codes: Count1=read.table("GENESFORANALYSIS.txt", sep="\t", header=TRUE) colnames(Count1) = paste...conditions = c(rep("T1", 3), rep("T2", 3), rep("T3", 3), rep("T4",3)) batch=c("A", "B", "A", "A", "A", "B", "A", "A", "B", …

edger

updated 5.2 years ago • chatterjee.arumoy

are differentially abundant between two or more groups of multiple samples in targeted metagenomic experiments. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities...on differential abundance detection. The paper: http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.2658.html The package: http://bioconductor.org/packages

Normalization metagenomeSeq Normalization metagenomeSeq

updated 12.2 years ago • Hector Corrada Bravo

The [RHCSA Training Institute][1] is your gateway to acquiring the essential skills and certifications needed to excel in this dynamic...field. At the RHCSA Training Institute, we are dedicated to providing top-notch training and guidance for the Red Hat Certified System Administrator...enter image description here][2] [1]: https://www.webasha.com/courses/rhcsa-online-training-institute-ce…

mgu74bv2cdf edge

updated 2.2 years ago • WebAsha

div class="preformatted">Extended draft paper submission: BCBGC-09 call for papers This Extended Call for Papers for the 2009 International Conference on Bioinformatics...09) (website: http://www.PromoteResearch.org ) is for those who didn't get a chance to submit the papers for the earlier call for papers. The papers received and accepted in response to this extended call for papers will...A…

updated 16.6 years ago • John Edward

automatically generate the DESeqDataSet and perform DESeq on the two groups to generate a results table. Because the samples have been collected and sequenced at different time in the past 5-6 years, I have included a `batch...counts, colData = metadata, design = ~ batch + group) ``` Where for `batch` I used the different sequenci…

deseq2

updated 5.6 years ago • alallo

done at different times, not just the library prep/sequencing). As a result, there is a significant batch effect, clearly visible in an MDS plot of edgeR-calculated logCPM values, and inter-batch contrasts always have many...for doing inter- batch comparisons with this dataset, but there is one saving grace: the batched time points are interleaved: batch A consists...up, then down, then up again)…

Normalization GO limma edgeR Normalization GO limma edgeR

updated 12.4 years ago • Ryan C. Thompson