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removeBatchEffect
•
reset
0
votes
2
replies
139
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
26 days ago
dqt
• 0
0
votes
5
replies
1.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 12 months ago by
ATpoint
★ 2.1k • written 22 months ago by
Xiaojie Cheng
• 0
0
votes
1
reply
394
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect
limma
updated 3.0 years ago by
Gordon Smyth
47k • written 3.0 years ago by
Sam
▴ 10
5
votes
7
replies
1.6k
views
logCPM to CPM conversion after removeBatchEffect()
edger
removeBatchEffect
cpm
logCPM
limma
3.7 years ago
altintas.ali
• 0
1
vote
6
replies
966
views
edgeR removing batch effect before using expression data for clustering
edger
r
batcheffect
clustering
removeBatchEffect
updated 3.7 years ago by
James W. MacDonald
62k • written 3.7 years ago by
Biologist
▴ 110
2
votes
5
replies
2.8k
views
Batch Effect Correction
batch effect
removebatcheffect
edgeR
rld
DEseq2
4.5 years ago
Antonio Ahn
▴ 10
1
vote
1
reply
1.0k
views
Batch effect removal before SC3?
SC3
batch effect
removebatcheffect
updated 5.2 years ago by
Vladimir Kiselev
▴ 150 • written 5.2 years ago by
muad.abdelhay
▴ 10
11
votes
8
replies
7.1k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 5.4 years ago by
Gordon Smyth
47k • written 5.4 years ago by
lirongrossmann
▴ 70
7
votes
8
replies
6.6k
views
removeBatchEffect options: design and covariates
limma
removebatcheffect
updated 5.4 years ago by
Gordon Smyth
47k • written 8.5 years ago by
Rao,Xiayu
▴ 550
0
votes
1
reply
1.9k
views
Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
sva
R
removebatcheffect
5.7 years ago
aina.jene
▴ 10
2
votes
2
replies
1.5k
views
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva
removebatcheffect
R
updated 5.7 years ago by
sina.nassiri
▴ 120 • written 5.7 years ago by
aina.jene
▴ 10
1
vote
3
replies
895
views
Re-use limma beta coefficients
limma
removebatcheffect
6.2 years ago
Keifa
▴ 10
3
votes
6
replies
1.5k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 6.3 years ago by
Jakub
▴ 50 • written 6.3 years ago by
amoltej
▴ 10
0
votes
3
replies
979
views
How to remove nested batch effects with removeBatchEffect?
edgeR
removeBatchEffect
nested design
updated 6.3 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
Jenny Drnevich
★ 2.0k
15
votes
7
replies
4.2k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 6.7 years ago by
Ryan C. Thompson
7.8k • written 6.7 years ago by
ompandey
▴ 10
4
votes
5
replies
2.0k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq
edger
ruvg
removebatcheffect
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
g.atla
▴ 10
9
votes
10
replies
11k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma
removeBatchEffect
heatmap
clustering
updated 7.1 years ago by
Bernd Klaus
▴ 600 • written 7.1 years ago by
Ekarl2
▴ 80
17 results • Page
1 of 1
Recent ...
Replies
Answer: struggling to create a heatmap
by
ATpoint
★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta
by
Michael Love
39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
by
ATpoint
★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2?
by
ATpoint
★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2?
by
Michael Love
39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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