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Showing :
BatchEffect
•
reset
3
votes
5
replies
852
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 7 months ago by
ATpoint
★ 4.1k • written 7 months ago by
Shashank
• 0
3
votes
4
replies
869
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
9 months ago • updated 8 months ago
Eva
▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 17 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
9
replies
357
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 8 days ago by
James W. MacDonald
65k • written 9 days ago by
Alexandre
• 0
2
votes
5
replies
1.3k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
Sara
• 0
2
votes
4
replies
629
views
Correct the batch effect in methylation analysis in R
BatchEffect
limma
methylationArrayAnalysis
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
kyj2226
• 0
2
votes
3
replies
1.1k
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 8 months ago by
James W. MacDonald
65k • written 8 months ago by
D-Bug
▴ 10
2
votes
4
replies
1.2k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2
RNASeq
BatchEffect
limma
updated 8 months ago by
Michael Love
41k • written 2.9 years ago by
athiebaut
• 0
2
votes
3
replies
1.1k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
amnahsiddiqa
▴ 10
2
votes
1
reply
263
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 9 weeks ago by
Michael Love
41k • written 9 weeks ago by
sap275
▴ 10
1
vote
2
replies
975
views
Batch effect between biological replicates
BatchEffect
DESeq2
11 months ago
gtechbio
▴ 10
1
vote
1
reply
454
views
Best way to handle batch effects from difference Mice?
RNASeqData
BatchEffect
edgeR
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
Sara
• 0
1
vote
1
reply
496
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
khaserdene99
• 0
1
vote
3
replies
360
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 8 weeks ago by
swbarnes2
★ 1.3k • written 9 weeks ago by
sap275
▴ 10
1
vote
4
replies
629
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
6 months ago
Wending
• 0
0
votes
0
replies
149
views
Can I combine collinear variables into a single value
BatchEffect
limma
9 weeks ago
Harrsha
• 0
0
votes
2
replies
616
views
smallRNA-seq analysis batch correction in limma
BatchEffect
limma
9 months ago
Eleonora
• 0
0
votes
0
replies
390
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
10 months ago
amnahsiddiqa
▴ 10
0
votes
5
replies
551
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 3 months ago by
ATpoint
★ 4.1k • written 4 months ago by
Xiao
• 0
0
votes
2
replies
208
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
14 days ago • updated 12 days ago
catv
• 0
0
votes
4
replies
595
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 17 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
1
reply
301
views
When should I correct for batch effects
BatchEffect
SingleCellExperiment
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
NeuroDaniel
• 0
0
votes
8
replies
399
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
8 weeks ago
michelafrancesconi8
• 0
0
votes
1
reply
621
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 8 months ago by
wrab425
• 0 • written 14 months ago by
snijesh
▴ 20
0
votes
1
reply
445
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 7 months ago by
ATpoint
★ 4.1k • written 7 months ago by
Giuseppe
• 0
25 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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