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svaseq
•
reset
0
votes
1
reply
588
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
20 months ago
Tongjun
• 0
0
votes
0
replies
1.1k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 2.2 years ago by
James W. MacDonald
65k • written 2.2 years ago by
Bex
• 0
0
votes
0
replies
755
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
2.5 years ago
georgia.katsoula
▴ 40
0
votes
1
reply
731
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
Mozart
▴ 30
1
vote
1
reply
887
views
svaseq - over adjustment
svaseq
sva
5.0 years ago
flippy23
• 0
1
vote
1
reply
848
views
sva correction for MEDIPS
MEDIPS
svaseq
sva
updated 5.2 years ago by
Lukas Chavez
▴ 570 • written 5.2 years ago by
tofukaj
• 0
2
votes
3
replies
1.5k
views
Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2
svaseq
5.2 years ago
bioinfo
• 0
3
votes
4
replies
1.4k
views
Calling svaseq() multiple times
edger
sva
svaseq
limma
updated 5.9 years ago by
Ryan C. Thompson
★ 7.9k • written 5.9 years ago by
cats_dogs
▴ 20
1
vote
2
replies
3.0k
views
Applying SVA to RNA-Seq dataset
DESeq2
sva
svaseq
batch effect correction
6.2 years ago
L_K
• 0
0
votes
0
replies
1.0k
views
correlated known batch effect correction using svaseq
svaseq
batcheffectcorrection
6.4 years ago
burcu.atasu
• 0
1
vote
1
reply
1.4k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 6.4 years ago by
davide risso
▴ 950 • written 6.4 years ago by
llo
▴ 10
0
votes
0
replies
1.2k
views
Batch correction with uncertain biological variables
sva
svaseq
batch effect
batch effects
batch effect correction
6.6 years ago
vedran.franke
• 0
1
vote
6
replies
1.7k
views
RNASeq fold change analysis after subtraction of contaminating MEF signal
deseq2
svaseq
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
gpalidwor
▴ 10
3
votes
4
replies
1.7k
views
Taking surrogate variable into account before running PCA
sva
svaseq
updated 6.8 years ago by
Guido Hooiveld
★ 3.9k • written 6.8 years ago by
wamiqsaifi
• 0
3
votes
2
replies
2.5k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma
sva
svaseq
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
Bogdan
▴ 670
2
votes
7
replies
1.7k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq
dexseq
updated 7.1 years ago by
Alejandro Reyes
★ 1.9k • written 7.1 years ago by
tofukaj
• 0
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 7.4 years ago by
Jakub
▴ 50 • written 7.4 years ago by
amoltej
▴ 10
5
votes
7
replies
5.1k
views
Correcting for known and surrogate variables in DESeq2
deseq2
svaseq
7.5 years ago
Akula, Nirmala NIH/NIMH [C]
▴ 190
2
votes
1
reply
1.6k
views
Regarding batch effect in Deseq2 package
deseq2
sva
svaseq
updated 7.6 years ago by
Michael Love
41k • written 7.6 years ago by
szenitha
▴ 20
0
votes
3
replies
2.4k
views
can we use sva function to estimate artifacts for rna seq data?
sva
svaseq
batcheffectcorrection
updated 7.6 years ago by
Jeff Leek
▴ 650 • written 7.6 years ago by
szenitha
▴ 20
1
vote
5
replies
3.6k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2
sva
svaseq
pca
7.8 years ago
Peter Alto
▴ 10
21 results • Page
1 of 1
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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