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SVA
•
reset
0
votes
8
replies
293
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
21 days ago
michelafrancesconi8
• 0
0
votes
3
replies
225
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 24 days ago by
James W. MacDonald
65k • written 27 days ago by
MEME
▴ 10
0
votes
5
replies
448
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 11 weeks ago by
Xiao
• 0
0
votes
1
reply
340
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
296
views
combat output NaN
sva
4 months ago
maxixian1990
• 0
0
votes
2
replies
434
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
5 months ago
Crystal571
• 0
5
votes
2
replies
620
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
6 months ago
Federico
▴ 10
5
votes
8
replies
1.1k
views
Batch correction and repeated measures
RUVSeq
sva
limma
6 months ago • updated 7 days ago
Jonathan
▴ 10
0
votes
1
reply
391
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
2
votes
3
replies
936
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
0
votes
2
replies
574
views
Fluidigm Data Batch Correction
sva
limma
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
Khushbu
• 0
3
votes
3
replies
826
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
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
0
votes
0
replies
351
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
1
vote
4
replies
1.8k
views
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
15 results • Page
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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…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
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
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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