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removebatcheffect
•
reset
0
votes
2
replies
907
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
769
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 5.0 years ago by
James W. MacDonald
65k • written 5.0 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
9
votes
8
replies
8.6k
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
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 7.0 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
5.9k
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
17 results • Page
1 of 1
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Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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