Showing : SVA • reset
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1.1k
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Error Combat (SVA)
sva
7.8 years ago alison.sara.waller • 0
0
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5
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1.6k
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Clarification regarding analysis with multi-factorial design
limma multiple factor design sva voom
7.9 years ago scanchi • 0
0
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0
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1.4k
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SVA/Combat without fitting an intercept
sva combat batch effect limma
8.0 years ago Eddie Imada • 0
1
vote
1
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2.1k
views
Limma with paired samples and SVA
limma sva duplicatecorrelation estimatecellcounts
updated 8.0 years ago by ★ 29k • written 8.0 years ago by • 0
9
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2
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2.3k
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Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
sva pca
updated 8.0 years ago by ▴ 120 • written 8.1 years ago by ★ 7.9k
2
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5
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3.9k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 8.1 years ago by ▴ 870 • written 8.1 years ago by • 0
2
votes
5
replies
7.8k
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RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 20
0
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1
reply
916
views
Retrieving corrected matrix after linear model adjustment
limma sva
updated 8.1 years ago by 68k • written 8.1 years ago by • 0
2
votes
2
replies
1.1k
views
Error in the fsva function after setting "newdat" argument to NULL
sva
updated 8.2 years ago by • 0 • written 8.4 years ago by ▴ 20
0
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0
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1.6k
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Batch correction with uncertain biological variables
sva svaseq batch effect batch effects batch effect correction
8.2 years ago vedran.franke • 0
1
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4
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2.4k
views
Finding the correct covariate for RNAseq experiment
deseq2 removebatcheffect() sva differential gene expression
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 110
0
votes
0
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1.7k
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Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
8.3 years ago DataFanatic ▴ 10
1
vote
6
replies
2.9k
views
normalization affects drastically limma-voom + sva results
normalization sva limma-voom
updated 8.3 years ago by 53k • written 8.3 years ago by ▴ 90
0
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7
replies
3.2k
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Applying sva is compatible with limma duplicateCorrelation?
limma-voom sva duplicatecorrelation
updated 8.3 years ago by ▴ 130 • written 8.3 years ago by ▴ 90
1
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1
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1.7k
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surrogate variables from sva independent of model variables?
sva
8.3 years ago pixie ▴ 10
4
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2
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4.2k
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Difference between "be" and "leek" methods when deciding number of surrogate variables to estimate with SVA?
sva num.sv
8.4 years ago brhead ▴ 40
3
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4
replies
2.3k
views
Taking surrogate variable into account before running PCA
sva svaseq
updated 8.4 years ago by ★ 4.1k • written 8.4 years ago by • 0
0
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1
reply
2.9k
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Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
sva R removebatcheffect
8.5 years ago aina.jene ▴ 10
0
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0
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967
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Is there any way to parallelise sva functions?
sva methylation
8.5 years ago stewart999 ▴ 10
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0
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1.2k
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SVA: Reference manual improvment
combat sva sva
8.5 years ago alice.anlind • 0
0
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3
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2.1k
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Using Combat function of SVA to remove known batch effect and using the result for down-stream analysis
sva batch effect deseq2 edgeR
updated 8.5 years ago by ★ 29k • written 8.5 years ago by ▴ 10
2
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2
replies
2.6k
views
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva removebatcheffect R
updated 8.5 years ago by ▴ 130 • written 8.5 years ago by ▴ 10
3
votes
3
replies
1.6k
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Subsetting ELists and Applying sva to Iterative Differential Gene Expression Tests
limma edgeR sva RNA-Seq
updated 8.5 years ago by 53k • written 8.5 years ago by • 0
2
votes
2
replies
2.8k
views
Pairwise differential expression analysis with batch effect using edgeR and SVA
edger rna-seq sva differential expression
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
1
vote
4
replies
2.5k
views
Using SVA with RRBS data
sva RRBS
updated 8.7 years ago by ▴ 650 • written 8.7 years ago by ▴ 10
0
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0
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1.5k
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RPKM counts with SVA package & Combat with SVA?
batch effect combat sva sva
8.7 years ago Ahdee ▴ 60
10
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4
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3.9k
views
Adjust for multiple batches using combat
combat sva limma
updated 8.7 years ago by ★ 29k • written 8.7 years ago by • 0
3
votes
2
replies
2.9k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma sva svaseq
updated 8.7 years ago by ★ 29k • written 8.7 years ago by ▴ 670
3
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4
replies
3.7k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 8.7 years ago by 43k • written 8.7 years ago by ▴ 10
0
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0
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1.5k
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How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
8.7 years ago Ryan C. Thompson ★ 7.9k
1
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1
reply
1.9k
views
sva: Parallel execution of sva()-function fails.
sva parallel
updated 8.8 years ago by 25k • written 8.8 years ago by ▴ 180
3
votes
1
reply
2.0k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 70
0
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4
replies
1.4k
views
Surrogate variables affecting just one sample?
sva
updated 8.8 years ago by ▴ 650 • written 8.8 years ago by ▴ 760
0
votes
4
replies
2.7k
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Using Bumphunter and SVA together in Minfi: bumphunterEngine nullMethod warning and FWER calculations
minfi sva bumphunter
8.9 years ago • updated 8.8 years ago brhead ▴ 40
0
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0
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1.4k
views
Bach effect and PEER/RUV correction on large population
methylation gene expression sva batch effect ruv
8.9 years ago carleshf ▴ 10
1
vote
1
reply
3.0k
views
Design formula for use with DESeq2 with SVA
deseq2 sva
8.9 years ago brookb • 0
1
vote
6
replies
3.1k
views
limma + voom + sva + complex RNA-seq design?
limma sva batch effect
8.9 years ago irenegallego • 0
1
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2
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1.6k
views
sva :: sva can variable of interest be a matrix itself?
sva variable of ineterest matrix
updated 8.9 years ago by ▴ 650 • written 8.9 years ago by • 0
6
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4
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2.0k
views
Combining newer/older RNAseq data, batch correcting
rnaseq limma sva batch effect voom
updated 9.0 years ago by ★ 29k • written 9.0 years ago by ▴ 10
4
votes
5
replies
3.7k
views
SVA and proportion of variance explained
sva svd explained variance pca
updated 9.0 years ago by ▴ 650 • written 9.1 years ago by ▴ 10
5
votes
3
replies
2.4k
views
Problem using sva with limma for microarray DE analysis
sva limma
updated 9.1 years ago by ▴ 610 • written 9.1 years ago by ▴ 40
0
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1
reply
1.6k
views
surrogate variable analysis using R package "sva"
sva r bioinformatics
updated 9.1 years ago by ▴ 760 • written 9.1 years ago by ▴ 10
0
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3
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2.2k
views
SVA package for RRBS - bisulfite methylation data
rrbs batch effect methylation sva
updated 9.1 years ago by • 0 • written 10.3 years ago by ▴ 20
5
votes
3
replies
4.6k
views
about SVA: matrix of corrected expression values
SVA COMBAT
9.1 years ago Bogdan ▴ 670
4
votes
3
replies
6.6k
views
svaseq: how many and which surrogate variables to pick
sva
updated 2.9 years ago by • 0 • written 10.2 years ago by ▴ 10
1
vote
1
reply
2.1k
views
Inspection of batch effect correction success with ComBat in R, regarding a merged dataset comprised of 4 different batches
affymetrix microarrays sva combat sva batch effect plotMDS
updated 9.2 years ago by ▴ 650 • written 9.2 years ago by ▴ 840
2
votes
1
reply
2.4k
views
Regarding batch effect in Deseq2 package
deseq2 sva svaseq
updated 9.2 years ago by 43k • written 9.2 years ago by ▴ 20
1
vote
2
replies
1.7k
views
Batch effect problem using SVA showing problems
SVA combat sva batch effect
updated 9.2 years ago by ▴ 650 • written 9.2 years ago by ▴ 10
2
votes
2
replies
7.1k
views
SVA: Error in svd((dats - rowMeans(dats))) : a dimension is zero
sva
updated 9.2 years ago by ▴ 650 • written 9.2 years ago by ▴ 30
1
vote
5
replies
2.4k
views
Paired design, normalisation and batch effects.
deseq2 eda sva rna-seq
updated 9.2 years ago by ▴ 610 • written 9.2 years ago by ▴ 10
240 results • Page 3 of 5
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Replies
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".
Answer: Suppress warning in RHDF5 write by James W. MacDonald 68k
``` > fun <- function() message("this is a message") > fun() this is a message > suppressMessages(fun()) > ```
Answer: Failure to download resources (MeSHDb) from AnnotationHub by shepherl 4.2k
apologies. These are contributed by someone outside the core team. On upload I did not realize they included the older Bioconductor storage…
Answer: "Watched Tags" are being erased rather than updated by shepherl 4.2k
This should now be resolved
Answer: Question about collapsing ASVs by genus level during DESeq2 analysis by Michael Love 43k
I'll just note that microbiome stats folks tend to use other tools than DESeq2. > several ASVs belong to the same genus but are not iden…
Votes
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Awards • All
Scholar to James W. MacDonald 68k
Popular Question to Daniel Cameron ▴ 40
Popular Question to Peter Hickey ▴ 760
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Popular Question to Fred Hutch (Recruiting) ▴ 40
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