Showing : SVA • reset
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Problem when trying to use \'affy\' package
Normalization GO affy sva SCAN.UPC Normalization GO affy sva SCAN.UPC
12.0 years ago Kaj Chokeshaiusaha ▴ 140
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1.3k
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Design matrix in Combat algorithm
sva sva
updated 12.0 years ago by ▴ 870 • written 12.0 years ago by ★ 13k
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2
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4.7k
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ComBat: Error when including numerical covariates in model (numCovs)
sva sva
updated 12.1 years ago by ▴ 20 • written 12.1 years ago by ▴ 870
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ComBat: Error when including numerical covariates in model (numCovs)
sva sva
12.1 years ago Jordan Ramsey ▴ 20
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1
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1.7k
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Questions on Combat in methylation data Thank you for your help
GO sva GO sva
updated 12.2 years ago by ▴ 440 • written 12.2 years ago by ▴ 870
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2
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1.5k
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Can't get ComBat in SVA running after SCAN.UPC
sva sva
12.4 years ago lep ▴ 90
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2.3k
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Remove batch effects from RNA-seq data using edgeR and sva/ComBat
sva sva
12.4 years ago Christopher Conley ▴ 40
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2
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6.1k
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sva + voom + limma
RNASeq Microarray sva RNASeq Microarray sva
updated 12.4 years ago by 53k • written 12.4 years ago by ▴ 120
12
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3
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sva: how to incorporate adjusting variables
inveRsion sva inveRsion sva
updated 12.4 years ago by ▴ 650 • written 12.4 years ago by ▴ 120
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1
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4.8k
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SVA package error message: Error in diag(dims[2]) - mod %*% solve(t(mod) %*% mod) %*% t(mod) : non-conformable arrays
sva sva
12.5 years ago Ying Chen ▴ 110
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2
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1.8k
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use Combat to adjust for hidden variables without knowing batch effect
Clustering sva Clustering sva
12.6 years ago W. Evan Johnson ▴ 870
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5
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2.1k
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use Combat to adjust for hidden variables without knowing batch effect
sva sva
12.6 years ago shirley zhang ★ 1.0k
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4
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2.2k
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FeatureExpressionSet using list.files() in place of read.xysfiles()
Microarray Annotation GO Organism probe annotate limma convert pdInfoBuilder sva GO sva
updated 12.6 years ago by ★ 4.3k • written 12.6 years ago by ▴ 140
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ComBat function (sva) generates very low adjusted p.values for a big number of genes
Microarray Normalization Clustering limma sva Microarray Normalization Clustering limma
12.7 years ago Alexandra Popa ▴ 10
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1.1k
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Error while executing ComBat from sva library in bioconductor
probe sva probe sva
12.7 years ago W. Evan Johnson ▴ 870
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971
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Error while executing ComBat from sva library in bioconductor
sva sva
12.7 years ago francesco.brundu@gmail.com ▴ 40
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2
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1.6k
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first time using combat
probe sva probe sva
updated 12.7 years ago by ▴ 10 • written 12.7 years ago by ▴ 870
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2.0k
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ComBat using SVA and bladderbatch package
Cancer sva Cancer sva
12.7 years ago Guest User ★ 13k
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1.1k
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Setting up design matrix in Limma
sva sva
12.8 years ago sanj ▴ 20
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2.3k
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sva: how to incorporate adjusting variables
inveRsion sva inveRsion sva
12.8 years ago Guest User ★ 13k
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809
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Bioconductor Digest, Vol 122, Issue 5
Microarray convert sva Microarray convert sva
12.8 years ago W. Evan Johnson ▴ 870
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2.6k
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sva: No significant surrogate variables
Microarray sva Microarray sva
12.9 years ago Shraddha Pai ▴ 80
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2.6k
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Problem with sva() probably stemming from model.matrix()
sva sva
12.9 years ago Guest User ★ 13k
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3
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2.9k
views
ComBat
Microarray sva Microarray sva
updated 13.1 years ago by ★ 6.8k • written 13.1 years ago by ▴ 20
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2
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1.8k
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SVA: problem loading on Windows
sva sva
updated 13.2 years ago by ★ 6.5k • written 13.2 years ago by ★ 4.1k
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2
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1.5k
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affy: batch completely confounded with treatment
sva sva
updated 13.5 years ago by ▴ 870 • written 13.5 years ago by ▴ 360
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1
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3.1k
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Back-estimating batch variables from SVA for ComBat?
sva sva
updated 13.5 years ago by ▴ 260 • written 13.5 years ago by ▴ 120
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0
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1.1k
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Back-estimating batch variables from SVA for ComBat?
sva sva
13.5 years ago wrighth ▴ 260
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2
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2.2k
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Surrogate variable analysis fails with “subscript out of bounds”
sva sva
updated 13.6 years ago by ▴ 650 • written 13.6 years ago by ▴ 20
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3
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2.7k
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batch effects 450K
Clustering Cancer Breast minfi sva Clustering Cancer Breast minfi sva
updated 13.7 years ago by ▴ 110 • written 13.7 years ago by ★ 13k
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2.8k
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SVA package: remove batch effects using ComBat
sva sva
13.8 years ago Tim Smith ★ 1.1k
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2
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2.8k
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Possible bug in sva package regarding ComBat and use of numCovs
Genetics sva Genetics sva
updated 14.0 years ago by ▴ 650 • written 14.0 years ago by ▴ 90
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2
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1.5k
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besides batch effects, whether adjust for specific quality metric variables (pos_control_mean, neg_control_mean, etc) in the analysis models
sva sva
updated 14.1 years ago by ★ 6.5k • written 14.1 years ago by ★ 1.0k
8
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3
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9.0k
views
Removing batch effects with sva and combat using the sva package
Regression limma sva Regression limma sva
updated 14.2 years ago by ▴ 60 • written 14.2 years ago by ▴ 650
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1
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1.9k
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Has anyone successfully used sva packages?
limma sva limma sva
updated 14.2 years ago by ▴ 60 • written 14.2 years ago by ▴ 970
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2.0k
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sva remove batch effect.
sva sva
14.2 years ago Fabrice Tourre ▴ 970
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5
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2.8k
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Problems installing sva and bladderbatch
sva sva
updated 14.2 years ago by 6.7k • written 14.2 years ago by ▴ 30
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7
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2.4k
views
sva package for R 2.13.1?
sva sva
updated 14.5 years ago by 68k • written 14.5 years ago by ▴ 110
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4
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4.9k
views
sva package
sva sva
updated 15.2 years ago by 21k • written 15.2 years ago by ▴ 90
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1.6k
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"No significant surrogate variables" for SVA (surrogate variable analysis)
sva sva
15.3 years ago Jack Luo ▴ 450
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1.6k
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Surrogate variable analysis (SVA) with Limma
GO limma sva GO limma sva
17.6 years ago Augusto Rendon ▴ 10
241 results • Page 5 of 5
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Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA by A.Barden ▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available by Tikaaa2sahaaaq2c • 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase by DamionLedner99 • 0
thanks for sharing!!! https://cran.r-project.org/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
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Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
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