Showing : batcheffect • reset
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 8 months ago by 50k • written 8 months ago by • 0
0
votes
2
replies
611
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
9 months ago Eleonora • 0
1
vote
3
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355
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 8 weeks ago by ★ 1.3k • written 8 weeks ago by ▴ 10
2
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4
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626
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
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 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
0
votes
5
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538
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
1
vote
2
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972
views
Batch effect between biological replicates
BatchEffect DESeq2
11 months ago gtechbio ▴ 10
2
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5
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1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 15 days ago by • 0 • written 10 months ago by • 0
0
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2
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193
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
13 days ago • updated 10 days ago catv • 0
3
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4
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863
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
1
vote
1
reply
452
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
0
votes
4
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591
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 16 days ago by 41k • written 6 months ago by • 0
1
vote
4
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622
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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
0
votes
1
reply
295
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 3 months ago by 65k • written 3 months ago by • 0
2
votes
1
reply
259
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 weeks ago by 41k • written 9 weeks ago by ▴ 10
0
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8
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396
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
8 weeks ago michelafrancesconi8 • 0
2
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3
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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
1
vote
1
reply
494
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
2
votes
4
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1.2k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 8 months ago by 41k • written 2.9 years ago by • 0
2
votes
9
replies
341
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 6 days ago by 65k • written 7 days ago by • 0
3
votes
5
replies
844
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
0
votes
1
reply
442
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
0
votes
1
reply
619
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
0
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0
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148
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Can I combine collinear variables into a single value
BatchEffect limma
8 weeks ago Harrsha • 0
0
votes
0
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389
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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
25 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 v1.35.0 by Michael Love 41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by James W. MacDonald 65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Answer: DESeq2 v1.35.0 by James W. MacDonald 65k
Odd release versions indicate a devel version, which upon release is incremented to the next even version, so you won't be able to find tha…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by fatinataly • 0
I tried also with oligo does not work, any other suggestion?
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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