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
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
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
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
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 7.2 years ago by
Alejandro Reyes
★ 1.9k • written 7.2 years ago by
tofukaj
• 0
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
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
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
41k • written 6.7 years ago by
gpalidwor
▴ 10
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 7.7 years ago by
Jeff Leek
▴ 650 • written 7.7 years ago by
szenitha
▴ 20
2
votes
1
reply
1.7k
views
Regarding batch effect in Deseq2 package
deseq2
sva
svaseq
updated 7.7 years ago by
Michael Love
41k • written 7.7 years ago by
szenitha
▴ 20
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
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
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
1
vote
1
reply
878
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
0
votes
1
reply
767
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
Mozart
▴ 30
0
votes
0
replies
784
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
2.6 years ago
georgia.katsoula
▴ 40
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
1
vote
1
reply
924
views
svaseq - over adjustment
svaseq
sva
5.1 years ago
flippy23
• 0
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
1
reply
630
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
22 months ago • updated 21 months ago
Tongjun
• 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
21 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
Awards
• All
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Zainab
• 0
Popular Question
to
Theo
▴ 10
Popular Question
to
gene_bioconductor
▴ 10
Popular Question
to
rohitsatyam102
▴ 20
Locations
• All
EMBL Heidelberg,
9 minutes ago
France,
12 minutes ago
The city by the bay,
36 minutes ago
WEHI, Melbourne, Australia,
47 minutes ago
Iran,
1 hour ago
Traffic: 517 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