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removebatcheffect
•
reset
0
votes
2
replies
898
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
15 months ago
dqt
• 0
0
votes
5
replies
3.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.3 years ago by
ATpoint
★ 4.0k • written 3.1 years ago by
Xiaojie Cheng
• 0
0
votes
1
reply
762
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect
limma
updated 4.2 years ago by
Gordon Smyth
50k • written 4.2 years ago by
Sam
▴ 10
5
votes
7
replies
2.6k
views
logCPM to CPM conversion after removeBatchEffect()
edger
removeBatchEffect
cpm
logCPM
limma
4.9 years ago
altintas.ali
• 0
1
vote
6
replies
1.6k
views
edgeR removing batch effect before using expression data for clustering
edger
r
batcheffect
clustering
removeBatchEffect
updated 4.9 years ago by
James W. MacDonald
65k • written 4.9 years ago by
Biologist
▴ 110
2
votes
5
replies
4.2k
views
Batch Effect Correction
batch effect
removebatcheffect
edgeR
rld
DEseq2
5.7 years ago
Antonio Ahn
▴ 10
1
vote
1
reply
1.5k
views
Batch effect removal before SC3?
SC3
batch effect
removebatcheffect
updated 6.4 years ago by
Vladimir Kiselev
▴ 150 • written 6.4 years ago by
muad.abdelhay
▴ 10
11
votes
8
replies
10k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 6.6 years ago by
Gordon Smyth
50k • written 6.6 years ago by
lirongrossmann
▴ 80
0
votes
1
reply
2.3k
views
Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
sva
R
removebatcheffect
6.9 years ago
aina.jene
▴ 10
2
votes
2
replies
2.0k
views
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva
removebatcheffect
R
updated 6.9 years ago by
sina.nassiri
▴ 130 • written 7.0 years ago by
aina.jene
▴ 10
1
vote
3
replies
1.3k
views
Re-use limma beta coefficients
limma
removebatcheffect
7.4 years ago
Keifa
▴ 10
3
votes
6
replies
2.2k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 7.5 years ago by
Jakub
▴ 50 • written 7.5 years ago by
amoltej
▴ 10
0
votes
3
replies
1.4k
views
How to remove nested batch effects with removeBatchEffect?
edgeR
removeBatchEffect
nested design
updated 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
Jenny Drnevich
★ 2.0k
17
votes
7
replies
5.8k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 7.9 years ago by
Ryan C. Thompson
★ 7.9k • written 7.9 years ago by
ompandey
▴ 10
4
votes
5
replies
2.6k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq
edger
ruvg
removebatcheffect
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
g.atla
▴ 10
9
votes
10
replies
13k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma
removeBatchEffect
heatmap
clustering
updated 8.3 years ago by
Bernd Klaus
▴ 610 • written 8.3 years ago by
Ekarl2
▴ 80
9
votes
8
replies
8.5k
views
removeBatchEffect options: design and covariates
limma
removebatcheffect
updated 6.6 years ago by
Gordon Smyth
50k • written 9.7 years ago by
Rao,Xiayu
▴ 550
17 results • Page
1 of 1
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Replies
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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