Showing : SVA • reset
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Design matrix in Combat algorithm
sva sva
updated 11.8 years ago by ▴ 870 • written 11.8 years ago by ★ 13k
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2
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4.6k
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ComBat: Error when including numerical covariates in model (numCovs)
sva sva
updated 11.8 years ago by ▴ 20 • written 11.8 years ago by ▴ 870
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ComBat: Error when including numerical covariates in model (numCovs)
sva sva
11.8 years ago Jordan Ramsey ▴ 20
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1
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1.6k
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Questions on Combat in methylation data Thank you for your help
GO sva GO sva
updated 11.9 years ago by ▴ 440 • written 11.9 years ago by ▴ 870
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2
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1.4k
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Can't get ComBat in SVA running after SCAN.UPC
sva sva
12.2 years ago lep ▴ 90
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2.2k
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Remove batch effects from RNA-seq data using edgeR and sva/ComBat
sva sva
12.2 years ago Christopher Conley ▴ 40
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2
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6.0k
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sva + voom + limma
RNASeq Microarray sva RNASeq Microarray sva
updated 12.2 years ago by 53k • written 12.2 years ago by ▴ 120
12
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3
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5.7k
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sva: how to incorporate adjusting variables
inveRsion sva inveRsion sva
updated 12.2 years ago by ▴ 650 • written 12.2 years ago by ▴ 120
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1
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4.7k
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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
12.2 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
12.3 years ago W. Evan Johnson ▴ 870
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5
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2.0k
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use Combat to adjust for hidden variables without knowing batch effect
sva sva
12.3 years ago shirley zhang ★ 1.0k
0
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4
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2.1k
views
FeatureExpressionSet using list.files() in place of read.xysfiles()
Microarray Annotation GO Organism probe annotate limma convert pdInfoBuilder sva GO sva
updated 12.4 years ago by ★ 4.3k • written 12.4 years ago by ▴ 140
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1.3k
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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
12.4 years ago Alexandra Popa ▴ 10
0
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1.1k
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Error while executing ComBat from sva library in bioconductor
probe sva probe sva
12.4 years ago W. Evan Johnson ▴ 870
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0
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938
views
Error while executing ComBat from sva library in bioconductor
sva sva
12.4 years ago francesco.brundu@gmail.com ▴ 40
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2
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1.5k
views
first time using combat
probe sva probe sva
updated 12.4 years ago by ▴ 10 • written 12.4 years ago by ▴ 870
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0
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2.0k
views
ComBat using SVA and bladderbatch package
Cancer sva Cancer sva
12.5 years ago Guest User ★ 13k
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1.1k
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Setting up design matrix in Limma
sva sva
12.6 years ago sanj ▴ 20
1
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2.2k
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sva: how to incorporate adjusting variables
inveRsion sva inveRsion sva
12.6 years ago Guest User ★ 13k
0
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0
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771
views
Bioconductor Digest, Vol 122, Issue 5
Microarray convert sva Microarray convert sva
12.6 years ago W. Evan Johnson ▴ 870
4
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2.6k
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sva: No significant surrogate variables
Microarray sva Microarray sva
12.6 years ago Shraddha Pai ▴ 80
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0
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2.5k
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Problem with sva() probably stemming from model.matrix()
sva sva
12.7 years ago Guest User ★ 13k
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3
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2.8k
views
ComBat
Microarray sva Microarray sva
updated 12.8 years ago by ★ 6.8k • written 12.9 years ago by ▴ 20
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2
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1.7k
views
SVA: problem loading on Windows
sva sva
updated 13.0 years ago by ★ 6.5k • written 13.0 years ago by ★ 4.1k
0
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2
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1.4k
views
affy: batch completely confounded with treatment
sva sva
updated 13.2 years ago by ▴ 870 • written 13.2 years ago by ▴ 360
0
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1
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3.0k
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Back-estimating batch variables from SVA for ComBat?
sva sva
updated 13.3 years ago by ▴ 260 • written 13.3 years ago by ▴ 120
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0
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1.0k
views
Back-estimating batch variables from SVA for ComBat?
sva sva
13.3 years ago wrighth ▴ 260
0
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2
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2.1k
views
Surrogate variable analysis fails with “subscript out of bounds”
sva sva
updated 13.4 years ago by ▴ 650 • written 13.4 years ago by ▴ 20
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3
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2.6k
views
batch effects 450K
Clustering Cancer Breast minfi sva Clustering Cancer Breast minfi sva
updated 13.4 years ago by ▴ 110 • written 13.4 years ago by ★ 13k
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0
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2.7k
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SVA package: remove batch effects using ComBat
sva sva
13.5 years ago Tim Smith ★ 1.1k
0
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2
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2.7k
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Possible bug in sva package regarding ComBat and use of numCovs
Genetics sva Genetics sva
updated 13.7 years ago by ▴ 650 • written 13.7 years ago by ▴ 90
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2
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1.4k
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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 13.9 years ago by ★ 6.5k • written 13.9 years ago by ★ 1.0k
8
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3
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8.5k
views
Removing batch effects with sva and combat using the sva package
Regression limma sva Regression limma sva
updated 13.9 years ago by ▴ 60 • written 13.9 years ago by ▴ 650
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1
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1.8k
views
Has anyone successfully used sva packages?
limma sva limma sva
updated 13.9 years ago by ▴ 60 • written 13.9 years ago by ▴ 970
1
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0
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1.9k
views
sva remove batch effect.
sva sva
13.9 years ago Fabrice Tourre ▴ 970
0
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5
replies
2.6k
views
Problems installing sva and bladderbatch
sva sva
updated 14.0 years ago by 6.7k • written 14.0 years ago by ▴ 30
0
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7
replies
2.3k
views
sva package for R 2.13.1?
sva sva
updated 14.2 years ago by 68k • written 14.2 years ago by ▴ 110
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4
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4.7k
views
sva package
sva sva
updated 15.0 years ago by 21k • written 15.0 years ago by ▴ 90
1
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0
replies
1.5k
views
"No significant surrogate variables" for SVA (surrogate variable analysis)
sva sva
15.0 years ago Jack Luo ▴ 450
0
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0
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1.6k
views
Surrogate variable analysis (SVA) with Limma
GO limma sva GO limma sva
17.4 years ago Augusto Rendon ▴ 10
240 results • Page 5 of 5
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Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset? by Kevin Blighe ★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be far…
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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