Newest 'batch-effects' Questions

3

votes

1answer

34 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 ...

batch-effects

asked Sep 30 '20 at 10:14

Sam

1355 bronze badges

0

votes

1answer

109 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, ...

asked Sep 13 '20 at 14:01

Sam

1355 bronze badges

3

votes

1answer

341 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 ...

rna-seq edger limma heatmap batch-effects

asked Aug 15 '20 at 12:54

Reza Rezaei

1696 bronze badges

0

votes

2answers

2k 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 ...

r batch-effects combat sva

asked Dec 2 '19 at 5:42

Mohammad

234 bronze badges

2

votes

2answers

860 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 ...

rna-seq limma batch-effects tpm

asked Sep 16 '19 at 14:57

Kent

1255 bronze badges

1

vote

2answers

254 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 ...

r rna-seq deseq2 pca batch-effects

asked Sep 15 '19 at 8:51

Exhausted

1,4815 silver badges20 bronze badges

1

vote

0answers

112 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 ...

batch-effects combat

asked May 8 '19 at 14:52

eric_kernfeld

3301 silver badge9 bronze badges

1

vote

1answer

88 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 ...

r microarray batch-effects

asked Feb 20 '19 at 11:32

krushnach Chandra

1,6024 silver badges15 bronze badges

3

votes

1answer

126 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 ...

rna-seq clustering batch-effects combat sva

asked Jan 3 '19 at 19:41

Kent

1255 bronze badges

3

votes

1answer

176 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. ...

rna-seq bioconductor batch-effects

asked Nov 28 '18 at 9:16

SmallChess

2,56912 silver badges30 bronze badges

2

votes

1answer

762 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 ...

r rna-seq deseq2 batch-effects sva

asked Oct 29 '18 at 21:33

Nikita Vlasenko

2,53811 silver badges30 bronze badges

0

votes

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 ...

r rna-seq edger batch-effects

asked Jul 25 '18 at 16:16

San

133 bronze badges

4

votes

3answers

2k 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 ...

rna-seq scrnaseq batch-effects merge

asked Feb 19 '18 at 17:25

gc5

1,8039 silver badges26 bronze badges

1

vote

2answers

1k 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 ...

rna-seq scrnaseq combat batch-effects

asked Feb 2 '18 at 16:01

gc5

1,8039 silver badges26 bronze badges

2

votes

1answer

102 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 ...

microarray quality-control data-preprocessing batch-effects

asked Feb 1 '18 at 21:21

bluemouse

1953 bronze badges

5

votes

1answer

803 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 ...

normalization scrnaseq imputation combat batch-effects

asked Jan 3 '18 at 20:22

gc5

1,8039 silver badges26 bronze badges

Stack Exchange Network

current community

your communities

more stack exchange communities

Questions tagged [batch-effects]

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

Details of DESeq2 modeling a batch effect

Removing Batch Effect in Heatmaps after Differential Gene Expression Analysis

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

TPM or rlog(CPM) for comparing expression?

Interpreting this PCA plot for RNA-seq

ComBat batch correction: understanding the model

Combat for multiplatform batch correction

sva for RNA-Seq data without known phenotype

How should I address batch effects in my experiment?

How to get the corrected matrix after SVA batch effect correction

Batch Effects in RNA Seq Sample

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

ComBat for batch effects removal on scRNA-seq data

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

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

Hot Network Questions

Questions tagged [batch-effects]

Related Tags