Showing : BatchEffect • reset
2
votes
9
replies
376
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 9 days ago by 65k • written 9 days ago by • 0
0
votes
2
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210
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
15 days ago • updated 12 days ago catv • 0
0
votes
8
replies
401
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
8 weeks ago michelafrancesconi8 • 0
1
vote
3
replies
361
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 8 weeks ago by ★ 1.3k • written 9 weeks ago by ▴ 10
0
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0
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149
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Can I combine collinear variables into a single value
BatchEffect limma
9 weeks ago Harrsha • 0
2
votes
1
reply
264
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 weeks ago by 41k • written 9 weeks ago by ▴ 10
0
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1
reply
301
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 3 months ago by 65k • written 3 months ago by • 0
0
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5
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560
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
2
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4
replies
630
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 4 months ago by 50k • written 4 months ago by • 0
1
vote
4
replies
631
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
6 months ago Wending • 0
0
votes
4
replies
599
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 18 days ago by 41k • written 6 months ago by • 0
0
votes
1
reply
446
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
3
votes
5
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855
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
2
votes
5
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1.3k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 8 months ago by 50k • written 8 months ago by • 0
2
votes
3
replies
1.1k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 8 months ago by 65k • written 8 months ago by ▴ 10
3
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4
replies
873
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago • updated 8 months ago Eva ▴ 10
0
votes
2
replies
616
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
9 months ago Eleonora • 0
1
vote
1
reply
455
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 10 months ago by 50k • written 10 months ago by • 0
2
votes
3
replies
1.1k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
0
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0
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390
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
10 months ago amnahsiddiqa ▴ 10
1
vote
1
reply
496
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
2
votes
5
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1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 17 days ago by • 0 • written 10 months ago by • 0
1
vote
2
replies
976
views
Batch effect between biological replicates
BatchEffect DESeq2
11 months ago gtechbio ▴ 10
0
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4
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904
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Combine RNA-seq
BatchEffect R rnaseq
updated 12 months ago by ★ 1.3k • written 12 months ago by • 0
2
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4
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1.4k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
12 months ago vk • 0
2
votes
2
replies
878
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 12 months ago by ★ 4.1k • written 12 months ago by ▴ 30
2
votes
3
replies
893
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.1k • written 13 months ago by ▴ 20
0
votes
1
reply
623
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 8 months ago by • 0 • written 14 months ago by ▴ 20
3
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2
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744
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
14 months ago chf • 0
2
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1
reply
1.4k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
1
reply
484
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 14 months ago by 41k • written 14 months ago by • 0
1
vote
1
reply
748
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 14 months ago by 65k • written 14 months ago by • 0
5
votes
2
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768
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Sva and batch effect
limma BatchEffect sva
updated 15 months ago by 50k • written 15 months ago by • 0
1
vote
1
reply
1.7k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 15 months ago by ★ 4.1k • written 15 months ago by ▴ 50
0
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0
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734
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
16 months ago Zhijie • 0
1
vote
0
replies
671
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
16 months ago r_grau ▴ 10
1
vote
2
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891
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 18 months ago by ★ 1.3k • written 18 months ago by • 0
3
votes
10
replies
1.9k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
19 months ago • updated 18 months ago eve.olszanowski • 0
1
vote
2
replies
791
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
19 months ago annamariabugaj ▴ 10
0
votes
1
reply
969
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 20 months ago by 41k • written 20 months ago by • 0
0
votes
1
reply
877
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 21 months ago by 50k • written 21 months ago by • 0
1
vote
1
reply
705
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 23 months ago by 41k • written 23 months ago by • 0
6
votes
7
replies
1.8k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
23 months ago • updated 22 months ago lmrogers34 ▴ 10
2
votes
1
reply
1.3k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 23 months ago by 50k • written 23 months ago by ▴ 30
0
votes
1
reply
935
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.1 years ago by 50k • written 2.1 years ago by • 0
1
vote
1
reply
1.1k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 2.2 years ago by ★ 4.1k • written 2.2 years ago by ▴ 30
0
votes
0
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505
views
Is it possible to do batch correction on Ht-Seq raw counts instead of using normalized counts? What's the difference?
Normalisedcounts Rawcounts Ht-SeqRNAData BatchEffect
2.2 years ago Ety • 0
1
vote
7
replies
1.3k
views
Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 2.2 years ago by 65k • written 2.2 years ago by ▴ 10
0
votes
2
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1.0k
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 2.3 years ago by ★ 13k • written 2.3 years ago by • 0
0
votes
2
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941
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Design formula in DESeq2
model BatchEffect hidden Design DESeq2
2.5 years ago m.glymenaki • 0
50 results • Page 1 of 1
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Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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