Showing : BatchEffect • reset
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
1 day ago Seungmin • 0
2
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9
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409
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 17 days ago by 65k • written 18 days ago by • 0
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2
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226
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
24 days ago • updated 21 days ago catv • 0
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8
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436
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
9 weeks ago michelafrancesconi8 • 0
1
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3
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377
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 10 weeks ago by ★ 1.4k • written 10 weeks ago by ▴ 10
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161
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Can I combine collinear variables into a single value
BatchEffect limma
10 weeks ago Harrsha • 0
2
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1
reply
272
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 weeks ago by 42k • written 11 weeks ago by ▴ 10
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1
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330
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 3 months ago by 65k • written 3 months ago by • 0
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5
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592
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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
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663
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 5 months ago by 50k • written 5 months ago by • 0
1
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4
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647
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
6 months ago Wending • 0
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4
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615
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 26 days ago by 42k • written 6 months ago by • 0
0
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1
reply
460
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Batch effect adjust in model matrix
BatchEffect edgeR
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
3
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5
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878
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
2
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5
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1.3k
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removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 9 months ago by 50k • written 9 months ago by • 0
2
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3
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1.1k
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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 9 months ago by 65k • written 9 months ago by ▴ 10
3
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4
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885
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
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2
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634
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
9 months ago Eleonora • 0
1
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1
reply
465
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
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3
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1.2k
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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
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396
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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
503
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
2
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5
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1.2k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 26 days ago by • 0 • written 11 months ago by • 0
1
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2
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989
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Batch effect between biological replicates
BatchEffect DESeq2
12 months ago gtechbio ▴ 10
0
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4
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915
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Combine RNA-seq
BatchEffect R rnaseq
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
2
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4
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1.5k
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How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
13 months ago vk • 0
2
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2
replies
897
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 13 months ago by ★ 4.1k • written 13 months ago by ▴ 30
2
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3
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914
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.1k • written 14 months ago by ▴ 20
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1
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627
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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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756
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Batch question Bulk RNA-Seq
BatchEffect RNASeq
14 months ago chf • 0
2
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1
reply
1.5k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
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1
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487
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Analysis with Batch correction
DESeq2 BatchEffect
updated 14 months ago by 42k • written 15 months ago by • 0
1
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1
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762
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Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 15 months ago by 65k • written 15 months ago by • 0
5
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2
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780
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Sva and batch effect
limma BatchEffect sva
updated 15 months ago by 50k • written 15 months ago by • 0
1
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1
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1.7k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 15 months ago by ★ 4.1k • written 15 months ago by ▴ 50
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0
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745
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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
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0
replies
682
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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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902
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Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
3
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10
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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
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2
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805
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
19 months ago annamariabugaj ▴ 10
0
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1
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986
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Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 20 months ago by 42k • written 21 months ago by • 0
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1
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882
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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
710
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 23 months ago by 42k • written 23 months ago by • 0
6
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7
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1.9k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
23 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
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1
reply
948
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
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0
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509
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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
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7
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1.3k
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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 2.4 years ago by ★ 13k • written 2.4 years ago by • 0
50 results • Page 1 of 1
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Comment: ChipQC 'names' attribute [9] must be the same length as the vector [2]' by bandconductor • 0
thanks! you have saved me so much time
Comment: Problem finding certain variables when importing a public database GSE73103 by Guido Hooiveld ★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
Comment: ChAMP installation issue by shepherl 3.9k
Without showing the commands you tried and the full output including error it is impossible to help. Please provide additional information…
Votes
Answer: ChipQC 'names' attribute [9] must be the same length as the vector [2]'
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
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