Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
Svaseq
•
reset
2
votes
2
replies
497
views
Double normalising when using sva and deseq2
DESeq2
Normalisation
Bulkrnaseq
Svaseq
6 months ago
BioinfGuru
▴ 70
0
votes
1
reply
854
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
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 2.9 years ago by
James W. MacDonald
67k • written 2.9 years ago by
Bex
• 0
0
votes
0
replies
984
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
960
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 4.7 years ago by
James W. MacDonald
67k • written 4.7 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 5.9 years ago by
Lukas Chavez
▴ 570 • written 5.9 years ago by
tofukaj
• 0
2
votes
3
replies
1.9k
views
Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2
svaseq
5.9 years ago
bioinfo
• 0
3
votes
4
replies
1.8k
views
Calling svaseq() multiple times
edger
sva
svaseq
limma
updated 6.6 years ago by
Ryan C. Thompson
★ 7.9k • written 6.6 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
6.9 years ago
L_K
• 0
0
votes
0
replies
1.3k
views
correlated known batch effect correction using svaseq
svaseq
batcheffectcorrection
7.1 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
7.4 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 7.4 years ago by
Michael Love
43k • written 7.4 years ago by
gpalidwor
▴ 10
3
votes
4
replies
2.0k
views
Taking surrogate variable into account before running PCA
sva
svaseq
updated 7.5 years ago by
Guido Hooiveld
★ 4.1k • written 7.5 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 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 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 7.9 years ago by
Alejandro Reyes
★ 1.9k • written 7.9 years ago by
tofukaj
• 0
3
votes
6
replies
2.8k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 8.2 years ago by
Jakub
▴ 50 • written 8.2 years ago by
amoltej
▴ 10
5
votes
7
replies
5.8k
views
Correcting for known and surrogate variables in DESeq2
deseq2
svaseq
8.2 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 8.4 years ago by
Jeff Leek
▴ 650 • written 8.4 years ago by
szenitha
▴ 20
1
vote
5
replies
4.0k
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
Recent ...
Replies
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character
by
ATpoint
★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format
by
ControlF5
• 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open!
by
Alan Downey
• 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
by
O'Brien
• 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts
by
O'Brien
• 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
Awards
• All
Popular Question
to
shepherl
4.1k
Popular Question
to
Gordon Smyth
52k
Popular Question
to
rohitsatyam102
▴ 20
Popular Question
to
Hervé Pagès
16k
Teacher
to
dsull
▴ 40
Locations
• All
University of Cambridge, UK | NIH Bethesda, MD,
just now
United States,
23 minutes ago
Sweden,
53 minutes ago
India,
1 hour ago
United States,
1 hour ago
Traffic: 557 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6