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SVAseq
•
reset
2
votes
2
replies
575
views
Double normalising when using sva and deseq2
DESeq2
Normalisation
Bulkrnaseq
Svaseq
8 months ago
BioinfGuru
▴ 70
0
votes
1
reply
889
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
2.6 years ago
Tongjun
• 0
0
votes
0
replies
1.3k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 3.1 years ago by
James W. MacDonald
68k • written 3.1 years ago by
Bex
• 0
0
votes
0
replies
1.0k
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
3.4 years ago
georgia.katsoula
▴ 40
0
votes
1
reply
999
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 4.8 years ago by
James W. MacDonald
68k • written 4.8 years ago by
Mozart
▴ 30
1
vote
1
reply
1.1k
views
svaseq - over adjustment
svaseq
sva
5.9 years ago
flippy23
• 0
1
vote
1
reply
1.1k
views
sva correction for MEDIPS
MEDIPS
svaseq
sva
updated 6.1 years ago by
Lukas Chavez
▴ 570 • written 6.1 years ago by
tofukaj
• 0
2
votes
3
replies
2.0k
views
Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2
svaseq
6.1 years ago
bioinfo
• 0
3
votes
4
replies
1.8k
views
Calling svaseq() multiple times
edger
sva
svaseq
limma
updated 6.7 years ago by
Ryan C. Thompson
★ 7.9k • written 6.7 years ago by
cats_dogs
▴ 20
1
vote
2
replies
3.8k
views
Applying SVA to RNA-Seq dataset
DESeq2
sva
svaseq
batch effect correction
7.1 years ago
L_K
• 0
0
votes
0
replies
1.3k
views
correlated known batch effect correction using svaseq
svaseq
batcheffectcorrection
7.3 years ago
burcu.atasu
• 0
1
vote
1
reply
1.7k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 7.3 years ago by
davide risso
▴ 980 • written 7.3 years ago by
llo
▴ 10
0
votes
0
replies
1.5k
views
Batch correction with uncertain biological variables
sva
svaseq
batch effect
batch effects
batch effect correction
7.5 years ago
vedran.franke
• 0
1
vote
6
replies
2.0k
views
RNASeq fold change analysis after subtraction of contaminating MEF signal
deseq2
svaseq
updated 7.5 years ago by
Michael Love
43k • written 7.5 years ago by
gpalidwor
▴ 10
3
votes
4
replies
2.1k
views
Taking surrogate variable into account before running PCA
sva
svaseq
updated 7.7 years ago by
Guido Hooiveld
★ 4.1k • written 7.7 years ago by
wamiqsaifi
• 0
3
votes
2
replies
2.8k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma
sva
svaseq
updated 8.0 years ago by
Aaron Lun
★ 28k • written 8.0 years ago by
Bogdan
▴ 670
2
votes
7
replies
2.1k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq
dexseq
updated 8.0 years ago by
Alejandro Reyes
★ 1.9k • written 8.0 years ago by
tofukaj
• 0
3
votes
6
replies
2.9k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 8.3 years ago by
Jakub
▴ 50 • written 8.3 years ago by
amoltej
▴ 10
5
votes
7
replies
6.0k
views
Correcting for known and surrogate variables in DESeq2
deseq2
svaseq
8.4 years ago
Akula, Nirmala NIH/NIMH [C]
▴ 190
2
votes
1
reply
2.1k
views
Regarding batch effect in Deseq2 package
deseq2
sva
svaseq
updated 8.5 years ago by
Michael Love
43k • written 8.5 years ago by
szenitha
▴ 20
0
votes
3
replies
2.9k
views
can we use sva function to estimate artifacts for rna seq data?
sva
svaseq
batcheffectcorrection
updated 8.5 years ago by
Jeff Leek
▴ 650 • written 8.5 years ago by
szenitha
▴ 20
1
vote
5
replies
4.1k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2
sva
svaseq
pca
8.7 years ago
Peter Alto
▴ 10
22 results • Page
1 of 1
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Answer: Automatically install dependencies
by
shepherl
4.1k
Since `BiocManager::install` is a wrapper around `install.packages` you should be able to use the dependencies argument. Default is the de…
Comment: For some reason I can't update BiocManager to 3.20
by
azm.ana2
• 0
Sorry i apologize for the delay. Thank you very much for the answer. I have two supervisers and the one who knows about the computer is com…
Comment: For some reason I can't update BiocManager to 3.20
by
azm.ana2
• 0
Sorry i apologize for the delay. Thank you very much for the answer. I have two supervisers and the one who knows about the computer is com…
Answer: SingleR with multiple single cell references
by
Aaron Lun
★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies
by
ATpoint
★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Votes
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
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