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svaseq
•
reset
0
votes
1
reply
193
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
6 months ago
Tongjun
• 0
0
votes
0
replies
544
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 12 months ago by
James W. MacDonald
62k • written 12 months ago by
Bex
• 0
0
votes
0
replies
402
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
16 months ago
georgia.katsoula
▴ 40
0
votes
1
reply
417
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 2.8 years ago by
James W. MacDonald
62k • written 2.8 years ago by
Mozart
▴ 20
1
vote
1
reply
595
views
svaseq - over adjustment
svaseq
sva
3.9 years ago
flippy23
• 0
1
vote
1
reply
569
views
sva correction for MEDIPS
MEDIPS
svaseq
sva
updated 4.0 years ago by
Lukas Chavez
▴ 570 • written 4.0 years ago by
tofukaj
• 0
2
votes
3
replies
782
views
Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2
svaseq
4.0 years ago
bioinfo
• 0
3
votes
4
replies
1.0k
views
Calling svaseq() multiple times
edger
sva
svaseq
limma
updated 4.7 years ago by
Ryan C. Thompson
7.8k • written 4.7 years ago by
cats_dogs
▴ 20
1
vote
2
replies
2.4k
views
Applying SVA to RNA-Seq dataset
DESeq2
sva
svaseq
batch effect correction
5.0 years ago
L_K
• 0
0
votes
0
replies
752
views
correlated known batch effect correction using svaseq
svaseq
batcheffectcorrection
5.2 years ago
burcu.atasu
• 0
1
vote
1
reply
1.0k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 5.3 years ago by
davide risso
▴ 920 • written 5.3 years ago by
llo
▴ 10
0
votes
0
replies
939
views
Batch correction with uncertain biological variables
sva
svaseq
batch effect
batch effects
batch effect correction
5.5 years ago
vedran.franke
• 0
1
vote
6
replies
1.3k
views
RNASeq fold change analysis after subtraction of contaminating MEF signal
deseq2
svaseq
updated 5.5 years ago by
Michael Love
39k • written 5.5 years ago by
gpalidwor
▴ 10
3
votes
4
replies
1.2k
views
Taking surrogate variable into account before running PCA
sva
svaseq
updated 5.6 years ago by
Guido Hooiveld
★ 3.5k • written 5.6 years ago by
wamiqsaifi
• 0
3
votes
2
replies
2.2k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma
sva
svaseq
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
Bogdan
▴ 660
2
votes
7
replies
1.3k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq
dexseq
updated 6.0 years ago by
Alejandro Reyes
★ 1.8k • written 6.0 years ago by
tofukaj
• 0
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
5
votes
7
replies
4.0k
views
Correcting for known and surrogate variables in DESeq2
deseq2
svaseq
6.3 years ago
Akula, Nirmala NIH/NIMH [C]
▴ 190
2
votes
1
reply
1.2k
views
Regarding batch effect in Deseq2 package
deseq2
sva
svaseq
updated 6.5 years ago by
Michael Love
39k • written 6.5 years ago by
szenitha
• 0
0
votes
3
replies
1.8k
views
can we use sva function to estimate artifacts for rna seq data?
sva
svaseq
batcheffectcorrection
updated 6.5 years ago by
Jeff Leek
▴ 640 • written 6.5 years ago by
szenitha
• 0
1
vote
5
replies
3.0k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2
sva
svaseq
pca
6.7 years ago
Peter Alto
▴ 10
21 results • Page
1 of 1
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Replies
Comment: TCGA: clinical data and expression data
by
sharifnstu1203002m
• 0
Hello, I am in the same problem. I downloaded "transcriptome profiling" data of TCGA by using the Bioconductor package. I get my gene expr…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
by
Jonathan Göke
▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
by
Gordon Smyth
47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user)
by
lalanis1
• 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma
by
Gordon Smyth
47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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James W. MacDonald
62k
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Michael Love
39k
Popular Question
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Gordon Smyth
47k
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Bogdan
▴ 660
Popular Question
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Martin Morgan
25k
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