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svaseq
•
reset
2
votes
2
replies
716
views
Double normalising when using sva and deseq2
DESeq2
Normalisation
Bulkrnaseq
Svaseq
10 months ago
BioinfGuru
▴ 70
0
votes
1
reply
935
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
2.8 years ago
Tongjun
• 0
0
votes
0
replies
1.4k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 3.3 years ago by
James W. MacDonald
68k • written 3.3 years ago by
Bex
• 0
0
votes
0
replies
1.1k
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
3.6 years ago
georgia.katsoula
▴ 40
0
votes
1
reply
1.1k
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 5.0 years ago by
James W. MacDonald
68k • written 5.0 years ago by
Mozart
▴ 30
1
vote
1
reply
1.2k
views
svaseq - over adjustment
svaseq
sva
6.1 years ago
flippy23
• 0
1
vote
1
reply
1.1k
views
sva correction for MEDIPS
MEDIPS
svaseq
sva
updated 6.2 years ago by
Lukas Chavez
▴ 570 • written 6.3 years ago by
tofukaj
• 0
2
votes
3
replies
2.1k
views
Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2
svaseq
6.3 years ago
bioinfo
• 0
3
votes
4
replies
1.9k
views
Calling svaseq() multiple times
edger
sva
svaseq
limma
updated 6.9 years ago by
Ryan C. Thompson
★ 7.9k • written 6.9 years ago by
cats_dogs
▴ 20
1
vote
2
replies
3.9k
views
Applying SVA to RNA-Seq dataset
DESeq2
sva
svaseq
batch effect correction
7.3 years ago
L_K
• 0
0
votes
0
replies
1.3k
views
correlated known batch effect correction using svaseq
svaseq
batcheffectcorrection
7.5 years ago
burcu.atasu
• 0
1
vote
1
reply
1.8k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 7.5 years ago by
davide risso
▴ 980 • written 7.5 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
7.7 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 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
gpalidwor
▴ 10
3
votes
4
replies
2.2k
views
Taking surrogate variable into account before running PCA
sva
svaseq
updated 7.9 years ago by
Guido Hooiveld
★ 4.1k • written 7.9 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 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 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 8.2 years ago by
Alejandro Reyes
★ 1.9k • written 8.2 years ago by
tofukaj
• 0
3
votes
6
replies
3.1k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 8.5 years ago by
Jakub
▴ 50 • written 8.5 years ago by
amoltej
▴ 10
5
votes
7
replies
6.2k
views
Correcting for known and surrogate variables in DESeq2
deseq2
svaseq
8.6 years ago
Akula, Nirmala NIH/NIMH [C]
▴ 190
2
votes
1
reply
2.2k
views
Regarding batch effect in Deseq2 package
deseq2
sva
svaseq
updated 8.7 years ago by
Michael Love
43k • written 8.7 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 8.7 years ago by
Jeff Leek
▴ 650 • written 8.7 years ago by
szenitha
▴ 20
1
vote
5
replies
4.2k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2
sva
svaseq
pca
8.9 years ago
Peter Alto
▴ 20
22 results • Page
1 of 1
Recent ...
Replies
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
donnycrimson
• 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Comment: CluserProfiler message "No gene can be mapped"
by
Carolina
• 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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