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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
4
votes
3
replies
1.5k
views
Blocked design and Surrogate Variables Analsysis(SVA)
limma
sva
block
updated 5 months ago by
stuartthafass
• 0 • written 7.8 years ago by
kodream
▴ 20
15 results • Page
1 of 1
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Replies
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
Comment: error running UniProt.ws
by
James W. MacDonald
60k
@marcelramos You have introduced a dependency on `BiocBaseUtils`, but that package is only available in devel.
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
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Gordon Smyth
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