Showing : SVA • reset
0
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3
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3.1k
views
can we use sva function to estimate artifacts for rna seq data?
sva svaseq batcheffectcorrection
updated 9.3 years ago by ▴ 650 • written 9.3 years ago by ▴ 20
0
votes
1
reply
1.6k
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
updated 9.3 years ago by ▴ 420 • written 9.3 years ago by ▴ 840
4
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2
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2.5k
views
PCA of bladderdata ("Batch effects and confounders" tutorial)
sva
updated 9.3 years ago by ▴ 180 • written 9.3 years ago by ▴ 20
0
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1
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1.6k
views
why my resultsNames(deseq) is not the same as model.matrix ?
deseq2 RNASeq SVA
updated 9.3 years ago by 43k • written 9.3 years ago by • 0
1
vote
5
replies
4.3k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2 sva svaseq pca
9.4 years ago Peter Alto ▴ 20
0
votes
2
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3.5k
views
Use surrogate variables on DESeq2
deseq2 sva deseq differential gene expression
updated 9.4 years ago by ▴ 20 • written 10.2 years ago by ▴ 40
1
vote
1
reply
2.4k
views
Null model in SVA for patient paired test comparing tumor vs normal
sva paired samples rnaseq
updated 9.5 years ago by ▴ 650 • written 9.5 years ago by • 0
0
votes
1
reply
2.3k
views
Adjusting microarray data using ComBat and SVA
sva sva
updated 9.5 years ago by • 0 • written 12.8 years ago by ▴ 40
2
votes
3
replies
1.9k
views
comBat/SVA with no "variable of interest" and two batches
combat sva covariates
updated 9.5 years ago by ▴ 420 • written 9.5 years ago by • 0
7
votes
3
replies
3.9k
views
SVA: Including variable of interest in ComBat model matrix
combat sva SVA sva ComBat batch effect
updated 9.5 years ago by ▴ 870 • written 9.5 years ago by ▴ 20
10
votes
10
replies
5.2k
views
Method for batch correction
combat sva limma
updated 9.6 years ago by ▴ 120 • written 9.6 years ago by ▴ 60
6
votes
6
replies
6.3k
views
Questions regarding SVA batch effect normalizazion into DeSeq2 workflow
sva deseq2 batch effect
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
1
vote
2
replies
3.0k
views
making ExpressionSet from RGList via NChannelSet for use with 'sva'
biobase convert sva ringo arrayqualitymetrics
updated 9.6 years ago by 53k • written 9.7 years ago by • 0
0
votes
1
reply
2.1k
views
Obtaining clean data after adjusting for batch effects using SVA
sva
9.7 years ago Momeneh Foroutan ▴ 10
2
votes
2
replies
1.9k
views
Paired analysis and batch effects ?
ruvseq sva edger
updated 9.7 years ago by ★ 7.9k • written 9.7 years ago by ▴ 10
1
vote
2
replies
2.4k
views
Evaluation of diagnostic plot resulted from ComBat function regarding batch effect correction of a merged microarray dataset
ComBat diagnostic plot batch effect affymetrix microarrays sva
updated 9.8 years ago by ▴ 870 • written 9.8 years ago by ▴ 840
0
votes
0
replies
2.3k
views
Appropriate implementation of ComBat function for known batch effect correction and alternative methodologies of merging microarray datasets
sva ComBat customcdf affymetrix microarrays limma
9.8 years ago svlachavas ▴ 840
0
votes
2
replies
4.0k
views
Using sva ComBat on DESeq2 Data
deseq2 DE rnaseq sva combat
updated 9.8 years ago by 43k • written 9.8 years ago by • 0
0
votes
6
replies
7.8k
views
ComBat with multiple batches
sva combat 450k
9.8 years ago ben.run974 • 0
9
votes
8
replies
7.5k
views
sva + egdeR - differential expression analysis - RNA-seq data
sva edgeR
9.9 years ago mrodrigues.fernanda ▴ 10
0
votes
1
reply
2.0k
views
RMA and ComBat for 2 batches with samples in common
microarray normalization sva
updated 9.9 years ago by ▴ 650 • written 9.9 years ago by • 0
3
votes
4
replies
6.0k
views
Running Combat in SVA with NA values in matrix
sva combat
9.9 years ago CC ▴ 10
5
votes
1
reply
2.4k
views
Quantile normalization + sva for microarray experiment
sva quantile normalization microarray
updated 9.9 years ago by ★ 7.9k • written 9.9 years ago by ▴ 50
0
votes
1
reply
2.1k
views
SomaticSignatures: negative entries after ComBat adjustment
sva somaticsignatures batch effect nmf
updated 9.9 years ago by ▴ 650 • written 10.0 years ago by • 0
10
votes
6
replies
12k
views
Estimating and removing batch effects from rna-seq dataset
sva batch effect rnaseq removebatcheffect() limma
updated 10.0 years ago by ▴ 650 • written 10.1 years ago by ▴ 110
1
vote
1
reply
3.0k
views
sva and svaseq for unsupervised analysis of expression data
sva combat gene expression batch effect rnaseq
updated 10.2 years ago by ▴ 650 • written 10.2 years ago by ▴ 10
0
votes
4
replies
1.9k
views
Reproducibility of results with ComBat
sva combat
updated 10.2 years ago by ▴ 650 • written 10.2 years ago by • 0
1
vote
2
replies
3.5k
views
Problem with n.sv in sva package
batch effect sva
10.3 years ago • updated 10.2 years ago daih • 0
1
vote
4
replies
4.2k
views
SVA package - for removing batch effect after DESeq - error in ComBat
sva combat
10.4 years ago GFM ▴ 20
2
votes
3
replies
2.1k
views
SVA batch effects for different technologies
normalization deseq2 sequencing sva
10.4 years ago marcin.bazyliszek • 0
2
votes
7
replies
2.9k
views
ComBat Error: in solve.default(t(des) %*% des) : System is computationally singuar: ...
ComBat sva
10.4 years ago edammer • 0
1
vote
1
reply
1.5k
views
Controlling for/removing batch effect
deseq2 sva
updated 10.5 years ago by 68k • written 10.5 years ago by ▴ 90
4
votes
8
replies
4.5k
views
Visualising effects of observation/sample weights in differential expression analysis
limma voom sva edgeR
updated 10.7 years ago by ▴ 1000 • written 10.7 years ago by ▴ 20
1
vote
1
reply
1.9k
views
ComBat (SVA) Application - Two Technical Effects
sva ComBat
updated 10.8 years ago by ▴ 610 • written 10.8 years ago by ▴ 370
0
votes
2
replies
3.1k
views
Remove batch effect - condition partially confounded by data
combat differential gene expression sva
updated 10.8 years ago by ▴ 650 • written 10.8 years ago by • 0
5
votes
12
replies
8.6k
views
Remove batch effect in small RNASeq study (SVA or others?)
RNASeq Alignment edgeR sva
updated 10.8 years ago by 53k • written 11.5 years ago by ★ 1.0k
0
votes
0
replies
1.3k
views
How can I use Combat correction parameters from one data set to adjust a new data set with the same batches
combat sva papramters
10.9 years ago p.yishai • 0
4
votes
4
replies
5.2k
views
sva::ComBat without covariate of interest?
sva combat
updated 11.0 years ago by ▴ 870 • written 11.0 years ago by ▴ 110
5
votes
2
replies
3.7k
views
ComBat - Including variable of interest in model matrix?
combat sva
updated 11.0 years ago by ▴ 650 • written 11.0 years ago by ▴ 10
4
votes
3
replies
2.5k
views
Blocked design and Surrogate Variables Analsysis(SVA)
limma sva block
updated 3.7 years ago by • 0 • written 11.0 years ago by ▴ 20
13
votes
11
replies
13k
views
RNA-Seq, generate batch-free count matrix
edgeR sva
updated 11.1 years ago by 53k • written 11.3 years ago by ▴ 90
0
votes
2
replies
2.5k
views
normalization and batch correction across multiple project
Normalization limma sva
updated 11.2 years ago by 53k • written 11.2 years ago by ▴ 220
0
votes
4
replies
1.8k
views
normalization and batch correction across multiple project
Normalization sva Normalization sva
updated 11.2 years ago by 53k • written 11.2 years ago by ▴ 220
0
votes
1
reply
4.9k
views
Steps of removing batch effects and hidden variables
RNASeq Normalization sva RNASeq Normalization sva
updated 11.3 years ago by ▴ 330 • written 11.3 years ago by ★ 1.0k
0
votes
0
replies
2.1k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
11.6 years ago Magda Price ▴ 60
1
vote
2
replies
2.7k
views
Surrogate Variable Analysis
sva sva
updated 11.6 years ago by ▴ 650 • written 11.6 years ago by ▴ 190
0
votes
8
replies
5.6k
views
ComBat: 3 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
updated 11.6 years ago by ★ 13k • written 11.6 years ago by ★ 13k
0
votes
0
replies
2.4k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
11.7 years ago W. Evan Johnson ▴ 870
0
votes
0
replies
2.1k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
11.7 years ago Magda Price ▴ 60
0
votes
0
replies
1.4k
views
Problem when trying to use \'affy\' package
Normalization GO affy sva SCAN.UPC Normalization GO affy sva SCAN.UPC
11.8 years ago Kaj Chokeshaiusaha ▴ 140
240 results • Page 4 of 5
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Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Kevin Blighe ★ 4.0k
Hello Matthew, Thanks for the detailed description-this sounds like a classic challenge in sncRNA analysis, where piRNAs (and other tsRN…
Answer: VariantAnnotation does escape = within header string quotes by Kevin Blighe ★ 4.0k
Hi, Thanks for the minimal reproduction - this is very clear and confirms a bug in `VariantAnnotation::writeVcf()`. The issue is that th…
Answer: Setting up a DESeq2 Design with Paired Data by Kevin Blighe ★ 4.0k
Hello, Your design formula looks mostly correct to me, but I believe that `vessel_n` should be `replicate` (or whatever unique identifie…
Comment: Failure to download resources (MeSHDb) from AnnotationHub by Steve Lianoglou ★ 13k
That fixed it, thanks Lori!
Comment: Suppress warning in RHDF5 write by nicolas.lhuillier • 0
Thanks a lot for the quick and effective reply. I had tried "suppressWarnings" but not "suppressMessages".
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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