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sva
•
reset
1
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4
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1.8k
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ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 5 months ago by
Hamza
• 0 • written 3.1 years ago by
zeegzaag
• 0
5
votes
8
replies
1.1k
views
Batch correction and repeated measures
RUVSeq
sva
limma
6 months ago • updated 7 days ago
Jonathan
▴ 10
2
votes
3
replies
1.0k
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
ATpoint
★ 4.0k • written 9 months ago by
amnahsiddiqa
▴ 10
2
votes
3
replies
940
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 7 months ago by
James W. MacDonald
65k • written 7 months ago by
D-Bug
▴ 10
3
votes
3
replies
830
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq
RNASeqData
sva
limma
9 months ago
amnahsiddiqa
▴ 10
5
votes
2
replies
624
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
6 months ago
Federico
▴ 10
0
votes
2
replies
577
views
Fluidigm Data Batch Correction
sva
limma
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
Khushbu
• 0
0
votes
5
replies
450
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 11 weeks ago by
ATpoint
★ 4.0k • written 12 weeks ago by
Xiao
• 0
0
votes
2
replies
436
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
5 months ago
Crystal571
• 0
0
votes
1
reply
392
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl
sva
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
Shila
• 0
0
votes
0
replies
354
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
9 months ago
amnahsiddiqa
▴ 10
0
votes
1
reply
343
views
DESeq2 interaction term + sva
sva
DESeq2
updated 12 weeks ago by
Michael Love
41k • written 3 months ago by
marinaw
▴ 20
0
votes
2
replies
298
views
combat output NaN
sva
4 months ago
maxixian1990
• 0
0
votes
8
replies
296
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
22 days ago • updated 21 days ago
michelafrancesconi8
• 0
0
votes
3
replies
227
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 24 days ago by
James W. MacDonald
65k • written 28 days ago by
MEME
▴ 10
15 results • Page
1 of 1
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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