Questions tagged [batch-effects]
The batch-effects tag has no usage guidance.
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1answer
29 views
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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40 views
Correcting for batch effect in bulk RNA seq datasets
I have samples from many different bulk RNA seq studies that exhibit an evident batch effect (samples from different labs cluster together regardless of treatment). I've found a lot of papers (here, ...
2
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1answer
60 views
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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0answers
65 views
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
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1answer
36 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 ...
0
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1answer
389 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, ...
3
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1answer
745 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 ...
0
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2answers
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
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2answers
1k 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 ...
0
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2answers
335 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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0answers
121 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
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1answer
97 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 ...
3
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1answer
165 views
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 ...
4
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1answer
206 views
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
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1answer
899 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 ...
0
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1answer
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 ...
5
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3answers
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 ...
2
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2answers
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 ...
2
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1answer
109 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 ...
6
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1answer
966 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 ...