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Svaseq
•
reset
2
votes
2
replies
954
views
Double normalising when using sva and deseq2
DESeq2
Normalisation
Bulkrnaseq
Svaseq
18 months ago
BioinfGuru
▴ 70
0
votes
1
reply
1.1k
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
3.4 years ago
Tongjun
• 0
0
votes
0
replies
1.6k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 3.9 years ago by
James W. MacDonald
68k • written 3.9 years ago by
Bex
• 0
0
votes
0
replies
1.2k
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
4.2 years ago
georgia.katsoula
▴ 40
0
votes
1
reply
1.2k
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 5.7 years ago by
James W. MacDonald
68k • written 5.7 years ago by
Mozart
▴ 30
1
vote
1
reply
1.3k
views
svaseq - over adjustment
svaseq
sva
6.7 years ago
flippy23
• 0
1
vote
1
reply
1.2k
views
sva correction for MEDIPS
MEDIPS
svaseq
sva
updated 6.9 years ago by
Lukas Chavez
▴ 570 • written 6.9 years ago by
tofukaj
• 0
2
votes
3
replies
2.4k
views
Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2
svaseq
6.9 years ago
bioinfo
• 0
3
votes
4
replies
2.2k
views
Calling svaseq() multiple times
edger
sva
svaseq
limma
updated 7.6 years ago by
Ryan C. Thompson
★ 7.9k • written 7.6 years ago by
cats_dogs
▴ 20
1
vote
2
replies
4.2k
views
Applying SVA to RNA-Seq dataset
DESeq2
sva
svaseq
batch effect correction
7.9 years ago
L_K
• 0
0
votes
0
replies
1.5k
views
correlated known batch effect correction using svaseq
svaseq
batcheffectcorrection
8.1 years ago
burcu.atasu
• 0
1
vote
1
reply
2.0k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 8.1 years ago by
davide risso
▴ 980 • written 8.1 years ago by
llo
▴ 10
0
votes
0
replies
1.6k
views
Batch correction with uncertain biological variables
sva
svaseq
batch effect
batch effects
batch effect correction
8.4 years ago
vedran.franke
• 0
1
vote
6
replies
2.3k
views
RNASeq fold change analysis after subtraction of contaminating MEF signal
deseq2
svaseq
updated 8.4 years ago by
Michael Love
43k • written 8.4 years ago by
gpalidwor
▴ 10
3
votes
4
replies
2.4k
views
Taking surrogate variable into account before running PCA
sva
svaseq
updated 8.5 years ago by
Guido Hooiveld
★ 4.1k • written 8.5 years ago by
wamiqsaifi
• 0
3
votes
2
replies
3.0k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma
sva
svaseq
updated 8.8 years ago by
Aaron Lun
★ 29k • written 8.8 years ago by
Bogdan
▴ 670
2
votes
7
replies
2.3k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq
dexseq
updated 8.9 years ago by
Alejandro Reyes
★ 1.9k • written 8.9 years ago by
tofukaj
• 0
3
votes
6
replies
3.5k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 9.2 years ago by
Jakub
▴ 50 • written 9.2 years ago by
amoltej
▴ 10
5
votes
7
replies
6.6k
views
Correcting for known and surrogate variables in DESeq2
deseq2
svaseq
9.2 years ago
Akula, Nirmala NIH/NIMH [C]
▴ 190
2
votes
1
reply
2.4k
views
Regarding batch effect in Deseq2 package
deseq2
sva
svaseq
updated 9.3 years ago by
Michael Love
43k • written 9.3 years ago by
szenitha
▴ 20
0
votes
3
replies
3.2k
views
can we use sva function to estimate artifacts for rna seq data?
sva
svaseq
batcheffectcorrection
updated 9.4 years ago by
Jeff Leek
▴ 650 • written 9.4 years ago by
szenitha
▴ 20
1
vote
5
replies
4.4k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2
sva
svaseq
pca
9.5 years ago
Peter Alto
▴ 20
22 results • Page
1 of 1
Recent ...
Replies
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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