Showing : batcheffect • reset
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2
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141
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
4 days ago • updated 1 day ago catv • 0
0
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8
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373
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 weeks ago michelafrancesconi8 • 0
1
vote
3
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337
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 7 weeks ago by ★ 1.3k • written 7 weeks ago by ▴ 10
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0
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140
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Can I combine collinear variables into a single value
BatchEffect limma
7 weeks ago Harrsha • 0
2
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1
reply
242
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 weeks ago by 41k • written 8 weeks ago by ▴ 10
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1
reply
266
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
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5
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512
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
2
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4
replies
605
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
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603
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
5 months ago Wending • 0
0
votes
4
replies
563
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 7 days ago by 41k • written 6 months ago by • 0
0
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1
reply
430
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
3
votes
5
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815
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
2
votes
5
replies
1.2k
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
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1.0k
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
votes
4
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846
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
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2
replies
591
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
9 months ago Eleonora • 0
1
vote
1
reply
442
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 9 months ago by 50k • written 9 months ago by • 0
2
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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 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
0
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0
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379
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
9 months ago amnahsiddiqa ▴ 10
1
vote
1
reply
481
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.0k • written 10 months ago by • 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 6 days ago by • 0 • written 10 months ago by • 0
1
vote
2
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952
views
Batch effect between biological replicates
BatchEffect DESeq2
11 months ago gtechbio ▴ 10
0
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4
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876
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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
851
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 12 months ago by ★ 4.0k • written 12 months ago by ▴ 30
2
votes
3
replies
870
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.0k • written 13 months ago by ▴ 20
0
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1
reply
606
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 8 months ago by • 0 • written 13 months ago by ▴ 20
3
votes
2
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718
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
13 months ago chf • 0
2
votes
1
reply
1.4k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
0
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1
reply
475
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 14 months ago by 41k • written 14 months ago by • 0
1
vote
1
reply
738
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
replies
754
views
Sva and batch effect
limma BatchEffect sva
updated 14 months ago by 50k • written 14 months ago by • 0
1
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1
reply
1.6k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 14 months ago by ★ 4.0k • written 15 months ago by ▴ 50
0
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0
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712
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
15 months ago Zhijie • 0
1
vote
0
replies
648
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
replies
871
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
18 months ago eve.olszanowski • 0
1
vote
2
replies
785
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
18 months ago annamariabugaj ▴ 10
0
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1
reply
948
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
855
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 20 months ago by 50k • written 21 months ago by • 0
1
vote
1
reply
693
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 22 months ago by 41k • written 22 months ago by • 0
6
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7
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1.8k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
22 months ago lmrogers34 ▴ 10
2
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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
909
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.0 years ago by 50k • written 2.0 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 ★ 4.0k • written 2.2 years ago by ▴ 30
0
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0
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496
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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
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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
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2
replies
921
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
2.5 years ago m.glymenaki • 0
6
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6
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1.4k
views
Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
2.5 years ago ary.lech ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by Gayatri • 0
What I meant is even after deleting the NCBI.sqlite file, and re-running the script, an empty NCBI.sqlite file (0 kb) is created which is c…
Comment: DESeq2 output used for PCA plot on R studio by ATpoint ★ 4.0k
> Increase variability for mutants: use larger subtractive modifiers I was thinking the same as swbarnes. You're doing some data munging h…
Comment: minfi::read.metharray.exp by Basti ▴ 780
This is indeed correct now !
Comment: get BM error by Fara • 0
Thank you for the reply. The examples are these. ENSGACG00000014473 ENSGACG00000015168 ENSGACG00000007529
Comment: get BM error by Mike Smith ★ 6.5k
Can you provide an example of the Ensemble IDs you're trying to convert?
Votes
Comment: get BM error
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
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