Showing : batcheffect • reset
2
votes
5
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1.3k
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
0
votes
2
replies
622
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
9 months ago Eleonora • 0
1
vote
3
replies
364
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 8 weeks ago by ★ 1.3k • written 9 weeks ago by ▴ 10
2
votes
4
replies
633
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
replies
566
views
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
1
vote
2
replies
979
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 19 days ago by • 0 • written 10 months ago by • 0
0
votes
2
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212
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
16 days ago • updated 14 days ago catv • 0
3
votes
4
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874
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
1
vote
1
reply
455
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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601
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 19 days ago by 41k • written 6 months ago by • 0
1
vote
4
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634
views
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
305
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
266
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 weeks ago by 41k • written 10 weeks ago by ▴ 10
0
votes
8
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404
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
8 weeks ago michelafrancesconi8 • 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 9 months ago by ▴ 10
1
vote
1
reply
496
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
389
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 10 days ago by 65k • written 11 days ago by • 0
3
votes
5
replies
859
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
447
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
623
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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151
views
Can I combine collinear variables into a single value
BatchEffect limma
9 weeks ago Harrsha • 0
0
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0
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391
views
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
Comment: Couldn't connect to server while using "pathways" by Michael Love 41k
You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site. Can you …
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Vincent J. Carey, Jr. 6.7k
btw that was run on M1 mac
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Vincent J. Carey, Jr. 6.7k
the test is not portable > aa <- aa_mutmat(acc = "MIYS930101", aaindex = "aaindex2") > str(aa) num [1:20, 1:20] 0.34 -0.0…
Comment: Method to find pathways different between 2 groups by Chris • 0
Sorry for not clear. I just try to find papers use this method for learning purpose. Which gives more context and detail examples, so I may…
Comment: Improving the design matrices vignette in RNAseq123 by Lluís Revilla Sancho ▴ 730
Cool. Thanks for looking into it.
Votes
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
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