Questions tagged [batch-effects]

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Batch correction in differential expression analysis

I have sent two sets (two batches in matter of sending for sequencing) of different samples (plasma) to small RNA-seq to Qiagen company This is how my meta data look ...
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Problems in conducting batch effect correction

I am now trying to conduct batch effect correction for my data matrix, whose samples (human) have different gender and come from different sequencing platforms. I have tried ...
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How to adjust by multiple variables using ComBat-Seq?

I am trying to adjust my RNA data using ComBat-Seq (from sva R package) since I realised that there are 3 batches that I need ...
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1 answer
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Can I Incorporate svaseq() into GSEA/GSVA analysis?

I understand GSEA/GSVA can take microarray-like expression matrix such as the output of voom() or vst(). However, I have a question on how we can also use svaseq() variables, correct the output from ...
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1 answer
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What is the best way to perform batch ajustment between two experiments?

I have duplicate drug efficacy experiments performed six months apart. I would like to know what is the right way to perform statistical analysis to understand fold changes after treatment with a drug....
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Subsetting with harmony

Currently merged two Seurat objects together and then ran Harmony for batch correction. Now I want to subset out a cell type of interest do I re run harmony or just do the standard PCA? ...
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1 answer
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What is the correct order of flooring-normalization-batch correction for microarrays?

This question was also asked on Biostars I am trying to learn and understand the correct order of data processing steps for microarrays. I have data which already was analyzed by a researcher using ...
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2 votes
2 answers
111 views

Comparing differential expression across samples - is batch effect correction needed?

I have a bulk RNA-seq dataset made up of control and treatment conditions for a range of cell lines. This dataset was generated in two batches, such that the cell lines are split between batches but ...
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1 answer
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References request: deciding what duplicate samples to include to avoid batch effects with previous studies

Suppose there is cohort with many samples to assay. In phase I of the project, subjects with a certain disease incidence and healthy controls were assayed. Now, in phase II of the project, we are ...
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1 answer
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(scRNA-seq) I have a dataset with 4 conditions (experiments) should I be anchoring aka integrating data for each comparison when looking for DEGs?

I have an experiment with 4 conditions in it two of them are controls. When I am correcting for batch effects (either with PCA or CCA) should I restrict my comparisons between particular groups? So ...
1 vote
0 answers
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Batch Effects that are Close to Collinear with Main Effect

Two years ago, I started working on a project uses both RNAseq and ATACseq. It's supposed to be a simple Healthy Control (HC) vs disease study. The sample collection was done in 2 phases, and it was ...
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-1 votes
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Assumptions of batch effect removal

What does removing a batch effect (e.g. with limma::removeBatchEffect) assume about the batch effect? Does it assume simply a constant batch effect for each level? ...
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2 votes
1 answer
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Batch effect correction using a subset of samples - using DE genes

I have some RNA-seq data with two very obvious batches as you can see in the PCA: The samples of interest (A - H) are from tumor tissues. In addition, there are data for two cell lines I and J. The ...
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How to use combat in order to remove batch effects?

I have RNA seq data and I need to use combat to remove the batch effects. Somehow when I run it, it isnt actually doing anything. The code: ...
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2 votes
1 answer
41 views

Should one be especially conscious of removing low counts, when applying batch correction?

When (as a mistake) I did not remove low counts at all (beside those that equal zero for all samples), I got the following ma plot (using Glimma) : On the right you see the individual counts. The ...
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1 answer
929 views

Details of DESeq2 modeling a batch effect

When correcting my data for a batch effect using removeBatchEffect, some of the gene expression values become negative. When searching for differentially expressed genes, I do not use the data above, ...
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3 votes
1 answer
1k views

Removing Batch Effect in Heatmaps after Differential Gene Expression Analysis

I'm working on a dataset in which the first replicate of each group is one batch and the second replicate is in a second batch. After checking the PCA plot and ...
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2 answers
3k views

how to solve “dim(X) must have a positive length” at running ComBat function in R

I used ComBat() for batch effect correction in my expression data. basically, that function inputs are expression data, Batch covariate, and Model matrix for the ...
2 votes
2 answers
2k views

TPM or rlog(CPM) for comparing expression?

I want to see the expression of a gene in a group of patient amongst the entire cohort using my RNA-Seq data. While I can do a differential expression analysis with limma or DESeq2, I want to see how ...
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2 answers
518 views

Interpreting this PCA plot for RNA-seq

I have RNA-seq from two sequencing batches; Lab technician says that he has run the RNA expression quantification two times in bathes 1 and 2 for example ...
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1 vote
0 answers
217 views

ComBat batch correction: understanding the model

A collaborator of mine is using ComBat for some RNA-seq data. I would like to understand what it's doing, and I have a specific question about the structure of the model. Equation 2.1 of the paper ...
2 votes
1 answer
139 views

Combat for multiplatform batch correction

I have been looking ways to use data from various micro-array platform such as agilient, rosetta/merk. Some of the established method I came across is combat, but I'm not sure if it can be done for ...
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3 votes
1 answer
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sva for RNA-Seq data without known phenotype

I have been working on RNA-Seq data from two different cohorts, and they show very strong batch effect (~35% variance explained by 1st component in PCA). Since I am trying to do a class discovery from ...
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4 votes
1 answer
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How should I address batch effects in my experiment?

Let's say I have an RNA-Seq experiment, where I'm interested in the significantly differentiated genes between pre-treatment and post-treatment conditions. "rep" == biological replicate. ...
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3 votes
1 answer
1k views

How to get the corrected matrix after SVA batch effect correction

I ran SVA to remove batch effects for my bulk RNAseq experiments, but now I need to somehow correct my data matrix in order to ...
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1 answer
1k views

Batch Effects in RNA Seq Sample

I am using the R (using EdgeR) for the RNA Seq analysis, I had few batch effect samples like Control vs treatment. Could anyone tell me the best way to remove the batch effects. I have looked into ...
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5 votes
3 answers
3k views

Is it possible to merge scRNAseq data from experiments with different design?

I have 4 different single-cell RNAseq experiments, each one representing a different sample of cell type population. I'd like to merge them to a single dataset. However, different cell types are ...
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2 votes
2 answers
2k views

ComBat for batch effects removal on scRNA-seq data

Is it possible to use sva's ComBat for batch effects removal on scRNA-seq data? Is there any difference between RNA-seq and scRNA-seq data which doesn't allow to use ComBat on single-cell data? (I am ...
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2 votes
1 answer
118 views

How hard is it to clean and QC gene expression microarray data?

I am a PhD student working on developing ideas for my dissertation papers. One of my planned papers will be working with some (human) gene expression data. I have had a class on working with gene ...
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6 votes
1 answer
1k views

Order of batch effects removal, data imputation and library size normalization in scRNA-seq data

I am preprocessing scRNA-seq data. What is the best practice in use to run both ComBat for batch effects removal, data imputation (to mitigate dropout) and library size normalization? I thought that ...
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