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 :
SVA
•
reset
0
votes
2
replies
75
views
DESeq2 LFC changes sign after adjusting for surrogates
sva
DESeq2
7 days ago • updated 4 days ago
Marie
• 0
2
votes
9
replies
343
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 19 days ago by
James W. MacDonald
60k • written 26 days ago by
Jasmin
• 0
1
vote
0
replies
148
views
Why does surrogate variable confound with variable given in mod?
sva
4 weeks ago
shdam
▴ 10
1
vote
3
replies
341
views
Error in shrinkage for DESeq2
sva
DESeq2
8 weeks ago
Kent
• 0
4
votes
3
replies
5.7k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 11 weeks ago by
wahaha
• 0 • written 4.8 years ago by
anton.kratz
▴ 60
1
vote
1
reply
123
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq
sva
DESeq2
updated 11 weeks ago by
James W. MacDonald
60k • written 11 weeks ago by
ramonfallon
• 0
1
vote
2
replies
238
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
12 weeks ago • updated 11 weeks ago
takemoto
• 0
0
votes
1
reply
161
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 4 months ago by
Gordon Smyth
46k • written 4 months ago by
Mageiros
• 0
1
vote
1
reply
247
views
How to determine if limma can adjust for batch effect
BatchEffect
limma
sva
DifferentialExpression
updated 5 months ago by
ATpoint
★ 1.4k • written 5 months ago by
nhaus
• 0
1
vote
4
replies
442
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2
sva
5 months ago
Clay
• 0
0
votes
0
replies
349
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 6 months ago by
James W. MacDonald
60k • written 6 months ago by
Bex
• 0
0
votes
5
replies
1.2k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 7 months ago by
ATpoint
★ 1.4k • written 16 months ago by
Xiaojie Cheng
• 0
0
votes
0
replies
290
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
10 months ago
georgia.katsoula
▴ 40
1
vote
4
replies
1.5k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat
sva
10 months ago
NewBioInfo
▴ 10
1
vote
2
replies
423
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva
limma
12 months ago
Ahdee
▴ 50
0
votes
1
reply
2.5k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA
combat sva
leek
updated 14 months ago by
chase.mateusiak
• 0 • written 5.3 years ago by
amoltej
▴ 10
0
votes
1
reply
607
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA
impute
sva
updated 15 months ago by
sebastian.lobentanzer
▴ 50 • written 15 months ago by
chiwut.wong
• 0
1
vote
3
replies
500
views
ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 17 months ago by
Kevin Blighe
3.6k • written 17 months ago by
zeegzaag
• 0
0
votes
1
reply
495
views
How to set mod0 in sva analysis
sva
updated 18 months ago by
Robert Castelo
★ 2.9k • written 18 months ago by
hank9cao
• 0
2
votes
2
replies
409
views
Preprocessing Issue
sva
RNASeq
Preprocessing
Normalization
BatchEffect
updated 18 months ago by
ATpoint
★ 1.4k • written 18 months ago by
MOHAMMAD
• 0
0
votes
0
replies
471
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
19 months ago
epibio
▴ 10
1
vote
8
replies
625
views
Error in running Combat function
sva
ComBat
updated 18 months ago by
Kevin Blighe
3.6k • written 19 months ago by
Reza
▴ 10
0
votes
5
replies
443
views
Variable of interest in combat correction
sva
combat
updated 21 months ago by
James W. MacDonald
60k • written 21 months ago by
ch_el
▴ 10
0
votes
3
replies
416
views
Extracting a subset of samples following SVA
Combat
SVA
Limma
updated 22 months ago by
Kevin Blighe
3.6k • written 23 months ago by
jonellevillar
• 0
0
votes
10
replies
526
views
Running SVA changes format of time variable in model
sva
proxitct
hms
updated 23 months ago by
James W. MacDonald
60k • written 23 months ago by
jonellevillar
• 0
7
votes
6
replies
571
views
sva ComBat implementation for multiple sources of batch effects
sva
combat
batch-adjustment
updated 2.3 years ago by
W. Evan Johnson
▴ 840 • written 2.3 years ago by
Zach Roe
▴ 10
0
votes
1
reply
304
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 2.3 years ago by
James W. MacDonald
60k • written 2.3 years ago by
Mozart
▴ 20
0
votes
1
reply
275
views
Adjusting for unwanted variation in DESeq2
DESeq2
deseq2
sva
rna-seq
differential expression anlaysis
updated 2.4 years ago by
James W. MacDonald
60k • written 2.4 years ago by
Nikolay Ivanov
• 0
1
vote
1
reply
389
views
SVA paired samples
SVA
EPIC
methylation
limma
updated 2.4 years ago by
James W. MacDonald
60k • written 2.5 years ago by
whyw6948
• 0
2
votes
4
replies
458
views
DESeq2 - problem with inferring correct results.
deseq2
rnaseq
sva
fdrtool
ihw
updated 2.5 years ago by
Michael Love
37k • written 2.5 years ago by
rihards.saksis
• 0
1
vote
2
replies
397
views
Validity of duplicateCorrelation after ComBat in this scenario
limma
ComBat
SVA
updated 2.6 years ago by
Gordon Smyth
46k • written 2.6 years ago by
vizio12341337
• 0
0
votes
0
replies
917
views
adjusting for batch using ComBat (sva) - singularity error
microarray
combat
sva
batch effects
2.6 years ago
anne.bozack
• 0
0
votes
1
reply
404
views
problem for interpretation of resulted ComBat() plot
ComBat
sva
batch effect
RNA-seq
updated 2.7 years ago by
W. Evan Johnson
▴ 840 • written 2.7 years ago by
modarzi
▴ 10
0
votes
0
replies
374
views
limma-voom group design and its effect on sva
limma
voom
group-design
sva
2.7 years ago
kentfung
• 0
0
votes
8
replies
566
views
Error in sva() function: missing values, NaNs produced
sva
batch-correction
updated 2.8 years ago by
James W. MacDonald
60k • written 2.8 years ago by
thkapell
▴ 10
0
votes
3
replies
477
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA
combat
r
microarray
covariates
updated 2.8 years ago by
Martin Morgan
25k • written 2.8 years ago by
dhwani2410
• 0
2
votes
5
replies
648
views
SVA for repeated measures design
SVA
deseq2
repeated measures
updated 2.9 years ago by
Robert Castelo
★ 2.9k • written 2.9 years ago by
sara.blocquiaux
• 0
0
votes
1
reply
495
views
Handling adjustment variables and surrogate variables in model
sva
deseq2
updated 2.9 years ago by
James W. MacDonald
60k • written 2.9 years ago by
rbutler
• 0
1
vote
1
reply
512
views
Bioconductor SVA: two variables of interest
sva
updated 2.9 years ago by
James W. MacDonald
60k • written 2.9 years ago by
sara.blocquiaux
• 0
4
votes
5
replies
452
views
Design matrix with intercept for multiple cluster comparison
limma
sva
updated 3.0 years ago by
centralmenu10
• 0 • written 3.0 years ago by
kentfung
• 0
0
votes
2
replies
444
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2
sva
combat
updated 3.0 years ago by
Michael Love
37k • written 3.0 years ago by
ege.dedeoglu
• 0
0
votes
3
replies
393
views
Design matrix for cohort with samples outside "block"
limma
voom
sva
3.0 years ago
kentfung
• 0
0
votes
0
replies
300
views
fsva function does not work without newdat argument
sva
3.0 years ago
jakob.wirbel
• 0
0
votes
0
replies
376
views
The correct specification of the model matrix to ComBat
ComBat
sva
3.0 years ago
Sam
▴ 10
7
votes
4
replies
2.5k
views
correcting the batch effects in Limma and SVA
limma
combat
sva
updated 3.1 years ago by
Gordon Smyth
46k • written 3.1 years ago by
Bogdan
▴ 640
0
votes
0
replies
519
views
Including sva results in SeqGSEA with data with batch effect
limma
deseq2
seqgsea
sva
deseq
3.1 years ago
kentfung
• 0
0
votes
1
reply
585
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq
sva
DSS
updated 3.2 years ago by
keegan
▴ 60 • written 3.2 years ago by
gjl
• 0
2
votes
8
replies
1.4k
views
removing batch effect using DESeq and sva
sva
deseq2
batch effect
PCA
heatmap
updated 3.2 years ago by
Michael Love
37k • written 3.2 years ago by
bioyas
▴ 10
2
votes
1
reply
824
views
Using SVA (surrogate variable analysis) to correct for 'completely' confounded cell type composition in DNA methylation data
sva
linear model
cell type composition
R
microarray
3.2 years ago
epibio
▴ 10
5
votes
3
replies
1.1k
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna
coexpression
sva
updated 3.2 years ago by
Peter Langfelder
★ 2.7k • written 3.2 years ago by
mikhael.manurung
▴ 260
50 results • Page
1 of 1
Recent ...
Replies
Comment: errors in annotation
by
Josie
• 0
OK thanks James. I'll send off an email to GenBank, see if they feel inclined to correct some errors.
Answer: Conversion of UniProt to Ensembl
by
James W. MacDonald
60k
I will provide an example below. But first, there is a vignette for biomaRt (actually two), and it has extensive examples of how to use the…
Comment: the difference between getGEO and getGEOSuppFiles
by
Fatemeh
• 0
thank you!
Answer: the difference between getGEO and getGEOSuppFiles
by
James W. MacDonald
60k
When submitting data to GEO, you are supposed to provide both the raw data and a matrix of processed data. When you use `getGEO` you get th…
Comment: error running UniProt.ws
by
James W. MacDonald
60k
https://www.bioconductor.org/checkResults/3.15/bioc-LATEST/UniProt.ws/nebbiolo1-install.html
Votes
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
Answer: the difference between getGEO and getGEOSuppFiles
Answer: the difference between getGEO and getGEOSuppFiles
Answer: TPM normalization starting with read counts
Awards
• All
Scholar
to
James W. MacDonald
60k
Popular Question
to
Matthew Ritchie
▴ 1000
Scholar
to
Thomas Carroll
▴ 410
Popular Question
to
rbenel
▴ 20
Popular Question
to
Gordon Smyth
46k
Locations
• All
WEHI, Melbourne, Australia,
just now
Canada,
3 minutes ago
United States,
9 minutes ago
United States,
11 minutes ago
Iraq,
13 minutes ago
Traffic: 292 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