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SVAseq
•
reset
5
votes
7
replies
5.2k
views
Correcting for known and surrogate variables in DESeq2
deseq2
svaseq
7.6 years ago
Akula, Nirmala NIH/NIMH [C]
▴ 190
2
votes
7
replies
1.8k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq
dexseq
updated 7.3 years ago by
Alejandro Reyes
★ 1.9k • written 7.3 years ago by
tofukaj
• 0
3
votes
6
replies
2.3k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 7.5 years ago by
Jakub
▴ 50 • written 7.5 years ago by
amoltej
▴ 10
1
vote
6
replies
1.7k
views
RNASeq fold change analysis after subtraction of contaminating MEF signal
deseq2
svaseq
updated 6.7 years ago by
Michael Love
42k • written 6.8 years ago by
gpalidwor
▴ 10
1
vote
5
replies
3.7k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2
sva
svaseq
pca
7.9 years ago
Peter Alto
▴ 10
3
votes
4
replies
1.5k
views
Calling svaseq() multiple times
edger
sva
svaseq
limma
updated 6.0 years ago by
Ryan C. Thompson
★ 7.9k • written 6.0 years ago by
cats_dogs
▴ 20
3
votes
4
replies
1.7k
views
Taking surrogate variable into account before running PCA
sva
svaseq
updated 6.9 years ago by
Guido Hooiveld
★ 3.9k • written 6.9 years ago by
wamiqsaifi
• 0
2
votes
3
replies
1.5k
views
Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2
svaseq
5.3 years ago
bioinfo
• 0
0
votes
3
replies
2.4k
views
can we use sva function to estimate artifacts for rna seq data?
sva
svaseq
batcheffectcorrection
updated 7.8 years ago by
Jeff Leek
▴ 650 • written 7.8 years ago by
szenitha
▴ 20
3
votes
2
replies
2.5k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma
sva
svaseq
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
Bogdan
▴ 670
1
vote
2
replies
3.1k
views
Applying SVA to RNA-Seq dataset
DESeq2
sva
svaseq
batch effect correction
6.3 years ago
L_K
• 0
0
votes
1
reply
642
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
22 months ago
Tongjun
• 0
1
vote
1
reply
1.5k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 6.5 years ago by
davide risso
▴ 950 • written 6.5 years ago by
llo
▴ 10
2
votes
1
reply
1.7k
views
Regarding batch effect in Deseq2 package
deseq2
sva
svaseq
updated 7.7 years ago by
Michael Love
42k • written 7.7 years ago by
szenitha
▴ 20
1
vote
1
reply
880
views
sva correction for MEDIPS
MEDIPS
svaseq
sva
updated 5.3 years ago by
Lukas Chavez
▴ 570 • written 5.3 years ago by
tofukaj
• 0
1
vote
1
reply
925
views
svaseq - over adjustment
svaseq
sva
5.1 years ago
flippy23
• 0
0
votes
1
reply
769
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 4.1 years ago by
James W. MacDonald
65k • written 4.1 years ago by
Mozart
▴ 30
0
votes
0
replies
1.1k
views
correlated known batch effect correction using svaseq
svaseq
batcheffectcorrection
6.5 years ago
burcu.atasu
• 0
0
votes
0
replies
1.2k
views
Batch correction with uncertain biological variables
sva
svaseq
batch effect
batch effects
batch effect correction
6.7 years ago
vedran.franke
• 0
0
votes
0
replies
1.1k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 2.3 years ago by
James W. MacDonald
65k • written 2.3 years ago by
Bex
• 0
0
votes
0
replies
790
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
2.6 years ago
georgia.katsoula
▴ 40
21 results • Page
1 of 1
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I have tried what you suggested. I started with methylation loci. I created segment1 and segment2 but how to combine them bec…
Comment: EGSEA usage with microarray data (with vooma)?
by
Chris
• 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results
by
swbarnes2
★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Mike Smith
★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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Michael Love
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▴ 10
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DevelopingHippo
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Robert Castelo
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