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svaseq
•
reset
2
votes
2
replies
533
views
Double normalising when using sva and deseq2
DESeq2
Normalisation
Bulkrnaseq
Svaseq
7 months ago
BioinfGuru
▴ 70
0
votes
1
reply
866
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
2.6 years ago • updated 2.5 years ago
Tongjun
• 0
0
votes
0
replies
1.3k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 3.0 years ago by
James W. MacDonald
67k • written 3.0 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
3.3 years ago
georgia.katsoula
▴ 40
0
votes
1
reply
981
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 4.8 years ago by
James W. MacDonald
67k • written 4.8 years ago by
Mozart
▴ 30
1
vote
1
reply
1.1k
views
svaseq - over adjustment
svaseq
sva
5.8 years ago
flippy23
• 0
1
vote
1
reply
1.0k
views
sva correction for MEDIPS
MEDIPS
svaseq
sva
updated 6.0 years ago by
Lukas Chavez
▴ 570 • written 6.0 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
6.0 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
3.7k
views
Applying SVA to RNA-Seq dataset
DESeq2
sva
svaseq
batch effect correction
7.0 years ago
L_K
• 0
0
votes
0
replies
1.3k
views
correlated known batch effect correction using svaseq
svaseq
batcheffectcorrection
7.2 years ago
burcu.atasu
• 0
1
vote
1
reply
1.7k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 7.2 years ago by
davide risso
▴ 980 • written 7.2 years ago by
llo
▴ 10
0
votes
0
replies
1.4k
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
1.9k
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
2.0k
views
Taking surrogate variable into account before running PCA
sva
svaseq
updated 7.6 years ago by
Guido Hooiveld
★ 4.1k • written 7.6 years ago by
wamiqsaifi
• 0
3
votes
2
replies
2.7k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma
sva
svaseq
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
Bogdan
▴ 670
2
votes
7
replies
2.0k
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
5.9k
views
Correcting for known and surrogate variables in DESeq2
deseq2
svaseq
8.3 years ago
Akula, Nirmala NIH/NIMH [C]
▴ 190
2
votes
1
reply
2.0k
views
Regarding batch effect in Deseq2 package
deseq2
sva
svaseq
updated 8.4 years ago by
Michael Love
43k • written 8.4 years ago by
szenitha
▴ 20
0
votes
3
replies
2.8k
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
8.6 years ago
Peter Alto
▴ 10
22 results • Page
1 of 1
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Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot
by
Quang NN
▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Prakash Sah
• 0
Thanks James!
Votes
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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