Showing : BatchEffect • reset
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 weeks ago • updated 5 weeks ago michelafrancesconi8 • 0
1
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3
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327
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 6 weeks ago by ★ 1.3k • written 6 weeks ago by ▴ 10
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134
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Can I combine collinear variables into a single value
BatchEffect limma
6 weeks ago Harrsha • 0
2
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1
reply
235
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 7 weeks ago by 41k • written 7 weeks ago by ▴ 10
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1
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245
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
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5
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490
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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
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592
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
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4
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592
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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
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4
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549
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 1 day ago by 41k • written 5 months ago by • 0
0
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1
reply
422
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Batch effect adjust in model matrix
BatchEffect edgeR
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
3
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5
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794
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
2
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5
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1.2k
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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
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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
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4
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837
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
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2
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580
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
9 months ago Eleonora • 0
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1
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440
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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
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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
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0
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374
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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
476
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 9 months ago by ★ 4.0k • written 9 months ago by • 0
2
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5
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 21 hours ago by • 0 • written 10 months ago by • 0
1
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2
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944
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Batch effect between biological replicates
BatchEffect DESeq2
11 months ago gtechbio ▴ 10
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4
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866
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Combine RNA-seq
BatchEffect R rnaseq
updated 11 months ago by ★ 1.3k • written 11 months ago by • 0
2
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4
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1.4k
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How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
12 months ago vk • 0
2
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2
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844
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Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 12 months ago by ★ 4.0k • written 12 months ago by ▴ 30
2
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3
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855
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
599
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
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2
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708
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Batch question Bulk RNA-Seq
BatchEffect RNASeq
13 months ago chf • 0
2
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1
reply
1.4k
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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
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463
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Analysis with Batch correction
DESeq2 BatchEffect
updated 14 months ago by 41k • written 14 months ago by • 0
1
vote
1
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724
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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 14 months ago by 65k • written 14 months ago by • 0
5
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2
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748
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Sva and batch effect
limma BatchEffect sva
updated 14 months ago by 50k • written 14 months ago by • 0
1
vote
1
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1.6k
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batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 14 months ago by ★ 4.0k • written 14 months ago by ▴ 50
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0
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699
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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
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0
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635
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
15 months ago r_grau ▴ 10
1
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2
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864
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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
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10
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1.8k
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Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
18 months ago eve.olszanowski • 0
1
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2
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778
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Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
18 months ago annamariabugaj ▴ 10
0
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1
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942
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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
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1
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849
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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 20 months ago by 50k • written 20 months ago by • 0
1
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1
reply
687
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
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1.2k
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removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 22 months ago by 50k • written 22 months ago by ▴ 30
0
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1
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896
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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
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1
reply
1.0k
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
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0
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492
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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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1.2k
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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
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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
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912
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
0
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1
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822
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Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data RNASeqR Normalization BatchEffect
updated 2.5 years ago by 65k • written 2.5 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: DESeq filtering specific to contrasts by Carlin95 • 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark by jacques.imbert • 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
Comment: Error in champ.load(): The following specified files do not exist by Basti ▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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