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Showing :
BatchEffect
•
reset
3
votes
5
replies
891
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
Shashank
• 0
3
votes
4
replies
892
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
9 months ago
Eva
▴ 10
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 4 weeks ago by
Ashley
• 0 • written 11 months ago by
zxc741xb
• 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 9 months ago by
James W. MacDonald
65k • written 9 months ago by
D-Bug
▴ 10
2
votes
4
replies
678
views
Correct the batch effect in methylation analysis in R
BatchEffect
limma
methylationArrayAnalysis
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
kyj2226
• 0
2
votes
9
replies
426
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
Alexandre
• 0
2
votes
5
replies
1.4k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Sara
• 0
2
votes
3
replies
1.2k
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
277
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 11 weeks ago by
Michael Love
42k • written 11 weeks ago by
sap275
▴ 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
42k • written 2.9 years ago by
athiebaut
• 0
1
vote
3
replies
386
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 10 weeks ago by
swbarnes2
★ 1.4k • written 11 weeks ago by
sap275
▴ 10
1
vote
1
reply
469
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
4
replies
658
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
1
vote
1
reply
508
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
khaserdene99
• 0
0
votes
0
replies
165
views
Can I combine collinear variables into a single value
BatchEffect
limma
11 weeks ago
Harrsha
• 0
0
votes
2
replies
643
views
smallRNA-seq analysis batch correction in limma
BatchEffect
limma
10 months ago
Eleonora
• 0
0
votes
0
replies
402
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
605
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 4 months ago by
ATpoint
★ 4.1k • written 4 months ago by
Xiao
• 0
0
votes
2
replies
237
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
28 days ago • updated 25 days ago
catv
• 0
0
votes
4
replies
628
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 4 weeks ago by
Michael Love
42k • written 6 months ago by
Crystal571
• 0
0
votes
2
replies
113
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 3 days ago by
zhouwanding
▴ 10 • written 5 days ago by
Seungmin
• 0
0
votes
1
reply
344
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
453
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
10 weeks ago
michelafrancesconi8
• 0
0
votes
1
reply
633
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 9 months ago by
wrab425
• 0 • written 14 months ago by
snijesh
▴ 20
0
votes
1
reply
466
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 7 months ago by
ATpoint
★ 4.1k • written 7 months ago by
Giuseppe
• 0
0
votes
0
replies
39
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
1 day ago
Shaimaa Gamal
• 0
26 results • Page
1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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