Showing : batch effect • reset
0
votes
0
replies
1.2k
views
which value from ruvadj in missMethyl can present methylation status
methylation missmethyl RUV batch effect
7.4 years ago RC • 0
1
vote
5
replies
1.6k
views
Comparing RNA-Seq expression data from different sequencers (HiSeq3000 and NovaSeq6000) - are there methods for batch effect corrections?
deseq2 rna-seq illumina batch effect
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 40
1
vote
3
replies
884
views
Differentially expressed genes detection between three classes with a batch effect in DESeq2
deseq2 batch effect differential gene expression
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
2
votes
5
replies
2.3k
views
Compare groups of different RNAseq sets
batch effect limma
updated 7.4 years ago by 53k • written 7.4 years ago by ▴ 370
3
votes
3
replies
1.8k
views
Difficulties with probable batch effect in paired blocked (treatment and placebo) experiment
deseq2 edger limma batch effect paired design
7.5 years ago Vladimir Krasikov ▴ 90
1
vote
4
replies
2.1k
views
Normalized counts after fitting linear model with batch effects - edgeR
edger batch effect normalized counts
updated 7.6 years ago by ★ 7.9k • written 7.6 years ago by • 0
1
vote
3
replies
3.9k
views
Batch effect removal with Deseq2
deseq2 batch effect removebatcheffect() limma
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 80
0
votes
2
replies
1.3k
views
Single and double mutant DEG analysis using DESeq2
deseq2 batch effect rnaseq
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
1
vote
1
reply
2.0k
views
Batch effect removal before SC3?
SC3 batch effect removebatcheffect
updated 7.8 years ago by ▴ 150 • written 7.8 years ago by ▴ 10
0
votes
3
replies
2.4k
views
How can I use DESeq2 for exploratory analysis after batch effect removal using RUVSeq?
deseq2 ruvseq rna-seq batch effect
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
1
vote
4
replies
3.6k
views
Remove batch effect using individuals as random in the model in Limma
batch effect Coeficents non estimable block random effects limma design matrix
updated 7.8 years ago by ★ 29k • written 7.8 years ago by ▴ 10
0
votes
0
replies
1.4k
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
7.9 years ago Eddie Imada • 0
6
votes
3
replies
7.6k
views
deseq2 correcting for batch effects
deseq2 batch effect removebatcheffect() design matrix
updated 7.9 years ago by 43k • written 7.9 years ago by ★ 1.5k
0
votes
2
replies
1.5k
views
Discrepancy in extracting contrasts
deseq2 resultsnames batch effect contrast
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
0
votes
0
replies
1.2k
views
Combined strand specific and unstranded samples
strand rnaseq differential gene expression batch effect counts
8.0 years ago lirongrossmann ▴ 80
0
votes
0
replies
1.6k
views
Batch correction with uncertain biological variables
sva svaseq batch effect batch effects batch effect correction
8.1 years ago vedran.franke • 0
1
vote
1
reply
1.8k
views
Scater normalizeExprs() batch effect
scater batch effect
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 30
0
votes
8
replies
8.0k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2 PCA batch effect
8.1 years ago pkachroo ▴ 10
2
votes
1
reply
1.3k
views
Plotting Gene Expression Data From Multiple Batches
batch effect microarray plot
updated 8.2 years ago by ★ 2.0k • written 8.2 years ago by ▴ 100
2
votes
1
reply
2.8k
views
Correcting for Batch Effects Prior to Differential Gene Expression Analysis with limma
limma batch effect rna-seq
updated 8.3 years ago by ★ 29k • written 8.3 years ago by • 0
2
votes
1
reply
1.4k
views
gene expression data analysis and batch effect methods
batch effect gene expression
updated 8.3 years ago by ▴ 420 • written 8.3 years ago by • 0
0
votes
0
replies
1.2k
views
gene expression data analysis and batch effect methods
batch effect gene expression
8.3 years ago tati6406 • 0
0
votes
3
replies
2.0k
views
Using Combat function of SVA to remove known batch effect and using the result for down-stream analysis
sva batch effect deseq2 edgeR
updated 8.3 years ago by ★ 29k • written 8.3 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Possible confounding of variable of interest with batch covariate and Partial NA coefficients when including batch in limma linear model for microarr…
limma batch effect design matrix microarray confounding
8.4 years ago svlachavas ▴ 840
0
votes
0
replies
1.6k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
8.4 years ago svlachavas ▴ 840
3
votes
4
replies
3.8k
views
Single cells batch effects
RUV single cell batch effect
8.5 years ago ribioinfo ▴ 100
3
votes
19
replies
4.7k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma batch effect covariates contrast differential gene expression
8.5 years ago mheydarpour ▴ 10
1
vote
1
reply
1.7k
views
Batch Correction and Normalization for champ.CNA
bioconductor ChAMP copy number batch effect normalization
updated 8.5 years ago by ▴ 10 • written 8.5 years ago by • 0
0
votes
0
replies
1.4k
views
RPKM counts with SVA package & Combat with SVA?
batch effect combat sva sva
8.5 years ago Ahdee ▴ 60
1
vote
2
replies
1.2k
views
Removinf Batch effect in EDGE-R
R edger batch effect
updated 8.6 years ago by ★ 29k • written 8.6 years ago by ▴ 40
6
votes
4
replies
1.9k
views
limma batch question
limma batch effect
8.6 years ago jalali4 • 0
0
votes
0
replies
1.4k
views
Bach effect and PEER/RUV correction on large population
methylation gene expression sva batch effect ruv
8.7 years ago carleshf ▴ 10
1
vote
6
replies
3.0k
views
limma + voom + sva + complex RNA-seq design?
limma sva batch effect
8.8 years ago irenegallego • 0
0
votes
2
replies
1.2k
views
can a batch effect be determined in edgeR with only 2 reps?
edger rnaseq batch effect read length
8.8 years ago Spollen, William G. ▴ 30
1
vote
2
replies
2.1k
views
is it possible to before and after batch effect removal from the data and see that batch effect removal actually worked
combat sva batch effect comba
updated 8.8 years ago by ▴ 120 • written 8.9 years ago by ▴ 10
6
votes
4
replies
1.9k
views
Combining newer/older RNAseq data, batch correcting
rnaseq limma sva batch effect voom
updated 8.9 years ago by ★ 29k • written 8.9 years ago by ▴ 10
1
vote
5
replies
1.3k
views
differential expression analysis in edgeR when you have 2 experiments and batch effect in 1 of the 2 experiments.
edger batch effect differential expression
8.9 years ago sezimmer • 0
0
votes
2
replies
1.9k
views
DESeq2 Model matrix design: Merging large RNAseq projects
deseq2 model.matrix batch effect rnaseq
8.9 years ago arom2 • 0
0
votes
3
replies
2.1k
views
SVA package for RRBS - bisulfite methylation data
rrbs batch effect methylation sva
updated 8.9 years ago by • 0 • written 10.1 years ago by ▴ 20
0
votes
3
replies
1.5k
views
Incorporate "batch" information for paired-design ?
RNA-Seq deseq2 batch effect
9.0 years ago g.atla ▴ 10
1
vote
1
reply
2.0k
views
Inspection of batch effect correction success with ComBat in R, regarding a merged dataset comprised of 4 different batches
affymetrix microarrays sva combat sva batch effect plotMDS
updated 9.0 years ago by ▴ 650 • written 9.1 years ago by ▴ 840
1
vote
2
replies
1.7k
views
Batch effect problem using SVA showing problems
SVA combat sva batch effect
updated 9.1 years ago by ▴ 650 • written 9.1 years ago by ▴ 10
5
votes
8
replies
11k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 16 months ago by • 0 • written 9.1 years ago by ▴ 30
0
votes
0
replies
978
views
Diffbind: blocking factors in a contrast not including all samples (bug?)
diffbind batch effect
9.1 years ago Jon Manning ▴ 90
0
votes
3
replies
1.4k
views
using technical replicates to batch correct
batch effect
9.1 years ago Juliet Hannah ▴ 360
14
votes
2
replies
3.8k
views
voom with combat
limma voom combat batch effect
updated 9.1 years ago by 53k • written 9.1 years ago by ▴ 10
6
votes
9
replies
2.1k
views
Interpretation of DE analysis results of an Illumina microarray dataset, and possible batch effect size problem
limma illumina microarray multifactorial design batch effect
updated 9.2 years ago by 53k • written 9.2 years ago by ▴ 90
2
votes
3
replies
1.9k
views
RNAseq outlier is a critical sample
rnaseq outlier statistics batch effect
updated 9.3 years ago by 53k • written 9.3 years ago by • 0
52
votes
20
replies
51k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 9.3 years ago by • 0 • written 9.8 years ago by ▴ 110
0
votes
0
replies
1.4k
views
SVA: Using ComBat for synthetic genetic array data
combat sva sga combat batch effect
9.4 years ago John Townsend ▴ 20
125 results • Page 2 of 3
Recent ...
Replies
Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Awards • All
Popular Question to rtrivedi1 ▴ 10
Popular Question to James W. MacDonald 68k
Popular Question to Assa Yeroslaviz ★ 1.5k
Popular Question to Nik dAK ▴ 10
Popular Question to Michael • 0
Locations • All
The city by the bay, 1 hour ago
Mexico, 3 hours ago
WEHI, Melbourne, Australia, 3 hours ago
United States, 5 hours ago
Spain, 8 hours ago
Traffic: 551 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6