Showing : BatchEffect • reset
2
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9
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 5 days ago by 65k • written 5 days ago by • 0
0
votes
2
replies
183
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
11 days ago • updated 8 days ago catv • 0
0
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8
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392
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
7 weeks ago michelafrancesconi8 • 0
1
vote
3
replies
351
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 8 weeks ago by ★ 1.3k • written 8 weeks ago by ▴ 10
0
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0
replies
146
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Can I combine collinear variables into a single value
BatchEffect limma
8 weeks ago Harrsha • 0
2
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1
reply
252
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
290
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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534
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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
2
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4
replies
624
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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617
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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 • updated 5 months ago Wending • 0
0
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4
replies
588
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 14 days ago by 41k • written 6 months ago by • 0
0
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1
reply
439
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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
votes
5
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837
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
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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
votes
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
3
votes
4
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860
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
0
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2
replies
607
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
9 months ago Eleonora • 0
1
vote
1
reply
450
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
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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
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0
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388
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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
492
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 13 days ago by • 0 • written 10 months ago by • 0
1
vote
2
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968
views
Batch effect between biological replicates
BatchEffect DESeq2
11 months ago gtechbio ▴ 10
0
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1
reply
617
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
2
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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
25 results • Page 1 of 1
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Replies
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma by James W. MacDonald 65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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