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<prev • 65 results • page 1 of 3 • next >
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How to avoid overfitting using SVA?
sva rna-seq overfitting written 4 weeks ago by Sam • 50
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173
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Surrogate variables in eQTL studies
sva deseq2 covariates eqtl gtex written 8 weeks ago by rodd • 130
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233
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DESeq2: vst() and varianceStabilizingTransformation()
R sva rna-seq normalization written 7 weeks ago by lenC_biotecLover • 0 • updated 7 weeks ago by Kevin Blighe ♦ 66k
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5 follow
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How to perform batch correction when we have only single condition?
batcheffects sva deseq2 combat written 3 months ago by svp • 240
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264
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Surrogate variable analysis: do I need to adjust all SVs?
sva methylation surrogate variable analysis written 5 months ago by wwyue127 • 10
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removing batch effects using ComBat and SVA
R sva combat batch effect written 4.4 years ago by LJ • 230 • updated 3 months ago by zhao03 • 30
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How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
R sva limma batch effect written 3 months ago by amirmehrgou • 0 • updated 3 months ago by RamRS ♦ 30k
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246
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Plotting PCA plot in DESeq2 on SVA corrected counts
sva deseq2 pca written 4 months ago by Mozart • 240
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182
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Comparison between heat maps corrected with different algorithms
sva written 4 months ago by Mozart • 240 • updated 4 months ago by Kevin Blighe ♦ 66k
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248
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Removing Unknown Batch Effects and Latent Confounders in Splicing PSI Data
sva differential expression splicing rna-seq limma written 5 months ago by eggerj • 0 • updated 5 months ago by geek_y ♦ 11k
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Question: Where can I download ALU, SVA and LINE1 Elements in fasta format?
sva alu line1 1000 genome project written 6 months ago by ncxhit • 0
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221
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Batch effect for SNP array
sva combat snp batch effect written 8 months ago by Taylor95 • 10 • updated 7 months ago by Biostar ♦♦ 20
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sva + egdeR - differential expression analysis - RNA-seq data
sva rna-seq edger written 4.8 years ago by mrodrigues.fernanda • 50 • updated 10 months ago by Biostar ♦♦ 20
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sva combat removes wanted biological variation
R sva combat rna-seq pca written 21 months ago by exin • 50 • updated 11 months ago by Biostar ♦♦ 20
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216
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In SVA, the percent of biological variable of interest didnot change after adding SV1.
R sva combat written 12 months ago by dhwani2410 • 0 • updated 12 months ago by Kevin Blighe ♦ 66k
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297
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Can I take 'organ type' as a batch effect and use ComBat to remove organ dependent variations?
sva batch effects combat rna-seq cross-species written 14 months ago by rodguinea • 0 • updated 14 months ago by i.sudbery ♦ 9.4k
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611
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Remove batch effect for many RNA-seq
sva combat rna-seq batch effect written 15 months ago by Shaway • 0
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304
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Strong covariates and weak biological signal in transcriptomes
R sva written 16 months ago by Agustin Gonzalez-Vicente • 70 • updated 16 months ago by zx8754 ♦ 9.7k
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820
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1
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pData function not found. substitute? "An end to end workflow for differential gene expression using Affymetrix microarrays"
R bioconductor pvca sva pdata written 17 months ago by RNAseqer • 140 • updated 17 months ago by zx8754 ♦ 9.7k
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820
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Principal component analysis of SVA's surrogate variables
sva stdev surrogate variables written 17 months ago by RNAseqer • 140 • updated 17 months ago by geek_y ♦ 11k
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689
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contrast matrix design question, limma-sva
sva contrast matrix limma written 17 months ago by RNAseqer • 140
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329
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sva pprob.b all 0s?
R sva pprob.b microarray written 17 months ago by RNAseqer • 140
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Using SVA to correct for covariates in RNA-seq data
R sva corrections covariates rna-seq written 19 months ago by sbrown669 • 20
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Question about sva + edgeR to identify differentially expressed genes
sva edger written 19 months ago by tujuchuanli • 80 • updated 19 months ago by ATpoint ♦ 40k
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svaseq and combat
combat sva effect batch written 3.4 years ago by Folder40g • 140 • updated 19 months ago by liull_hust • 0
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349
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sva correction for MEDIPS
medip-seq sva svaseq medips written 21 months ago by tofukaj • 10
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745
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ComBat correction with one batch containing only one sample - keep or remove?
proteome sva combat R written 23 months ago by Sebastian Hesse • 180 • updated 21 months ago by Biostar ♦♦ 20
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576
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Normalise batch effects for Percent Spliced In (PSI) matrice
sva combat splicing written 21 months ago by ZheFrench • 300
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5 follow
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sva output interpretation
sva rna-seq written 2.1 years ago by elb • 190 • updated 2.1 years ago by Devon Ryan ♦ 97k
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7 follow
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Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
R sva deseq2 batch effects written 2.2 years ago by Kristin Muench • 530 • updated 2.2 years ago by Teresa • 20
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