Showing : SVA • reset
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1.9k
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SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 22 days ago by • 0 • written 4.1 years ago by ▴ 10
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1
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113
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 26 days ago by ▴ 50 • written 26 days ago by • 0
0
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2
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206
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How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
12 weeks ago • updated 11 weeks ago Xiaojie Cheng • 0
0
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3
replies
186
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ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 3 months ago by 3.1k • written 3 months ago by • 0
0
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1
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106
views
How to set mod0 in sva analysis
sva
updated 4 months ago by ★ 2.7k • written 4 months ago by • 0
2
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2
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154
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Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4 months ago by ▴ 640 • written 4 months ago by • 0
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0
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215
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
4 months ago Papyrus ▴ 10
1
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8
replies
304
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Error in running Combat function
sva ComBat
updated 4 months ago by 3.1k • written 5 months ago by ▴ 10
0
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5
replies
158
views
Variable of interest in combat correction
sva combat
updated 7 months ago by 57k • written 7 months ago by ▴ 10
0
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3
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194
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Extracting a subset of samples following SVA
Combat SVA Limma
updated 8 months ago by 3.1k • written 8 months ago by • 0
0
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10
replies
205
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Running SVA changes format of time variable in model
sva proxitct hms
updated 9 months ago by 57k • written 9 months ago by • 0
7
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6
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233
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sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 13 months ago by ▴ 840 • written 13 months ago by ▴ 10
0
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1
reply
111
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 14 months ago by 57k • written 14 months ago by ▴ 20
0
votes
1
reply
125
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 15 months ago by 57k • written 15 months ago by • 0
1
vote
1
reply
120
views
SVA paired samples
SVA EPIC methylation limma
updated 15 months ago by 57k • written 15 months ago by • 0
2
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4
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180
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DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 16 months ago by 33k • written 16 months ago by • 0
1
vote
2
replies
162
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 17 months ago by 43k • written 17 months ago by • 0
0
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0
replies
399
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
17 months ago anne.bozack • 0
0
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1
reply
193
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 18 months ago by ▴ 840 • written 18 months ago by ▴ 10
0
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0
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166
views
limma-voom group design and its effect on sva
limma voom group-design sva
18 months ago kentfung • 0
0
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8
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247
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 19 months ago by 57k • written 19 months ago by ▴ 10
0
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3
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231
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 19 months ago by 25k • written 19 months ago by • 0
2
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5
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354
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 20 months ago by ★ 2.7k • written 21 months ago by • 0
0
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1
reply
243
views
Handling adjustment variables and surrogate variables in model
sva deseq2
updated 21 months ago by 57k • written 21 months ago by • 0
1
vote
1
reply
251
views
Bioconductor SVA: two variables of interest
sva
updated 21 months ago by 57k • written 21 months ago by • 0
4
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5
replies
287
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 21 months ago by • 0 • written 21 months ago by • 0
0
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2
replies
211
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 22 months ago by 33k • written 22 months ago by • 0
0
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3
replies
224
views
Design matrix for cohort with samples outside "block"
limma voom sva
22 months ago kentfung • 0
0
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0
replies
157
views
fsva function does not work without newdat argument
sva
22 months ago jakob.wirbel • 0
0
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0
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237
views
The correct specification of the model matrix to ComBat
ComBat sva
22 months ago Sam ▴ 10
7
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4
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1.4k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 23 months ago by 43k • written 23 months ago by ▴ 610
0
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0
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273
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
23 months ago kentfung • 0
0
votes
1
reply
303
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq sva DSS
updated 24 months ago by ▴ 60 • written 2.0 years ago by • 0
1
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8
replies
714
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 2.0 years ago by 33k • written 2.0 years ago by • 0
2
votes
1
reply
413
views
Using SVA (surrogate variable analysis) to correct for 'completely' confounded cell type composition in DNA methylation data
sva linear model cell type composition R microarray
2.0 years ago Papyrus ▴ 10
5
votes
3
replies
548
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna coexpression sva
updated 2.1 years ago by ★ 2.6k • written 2.1 years ago by ▴ 230
0
votes
1
reply
250
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 2.1 years ago by 33k • written 2.1 years ago by ▴ 20
3
votes
12
replies
991
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 2.1 years ago by 57k • written 2.1 years ago by ▴ 10
1
vote
1
reply
292
views
svaseq - over adjustment
svaseq sva
2.2 years ago flippy23 • 0
0
votes
8
replies
405
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 2.2 years ago by 33k • written 2.2 years ago by • 0
1
vote
2
replies
457
views
Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 2.3 years ago by ▴ 80 • written 2.3 years ago by ▴ 10
4
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4
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623
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 570
0
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0
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454
views
OpenBLAS issue with ComBat() function of the R SVA package on Torque cluster
sva R OpenBLAS
updated 2.3 years ago by 57k • written 2.3 years ago by • 0
4
votes
2
replies
3.9k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 2.4 years ago by • 0 • written 3.7 years ago by ▴ 60
1
vote
1
reply
335
views
sva correction for MEDIPS
MEDIPS svaseq sva
updated 2.4 years ago by ▴ 550 • written 2.4 years ago by • 0
0
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7
replies
523
views
paired sample - SVA model matrix
limma sva paired sample
updated 2.5 years ago by 57k • written 2.5 years ago by • 0
1
vote
1
reply
498
views
Define batch effect variables before removing them or getting rid of hidden surrogate variables
batch effect correction sva proteomics
2.6 years ago Sebastian Hesse ▴ 50
1
vote
10
replies
2.0k
views
SVAseq and DESeq2 workflow
sva deseq2
updated 2.7 years ago by 33k • written 2.7 years ago by • 0
0
votes
0
replies
276
views
Sva for tumor cellular heterogeneity
limma sva
2.7 years ago chp950 • 0
0
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2
replies
585
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 2.7 years ago by 33k • written 2.7 years ago by • 0
50 results • Page 1 of 1
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Comment: DESeq2 - one groups with no replicates by SUMIT • 0
I disturb you only because I thought why I am not getting an error like deprecated in v1.20 and no longer supported...... Anyway, Thank you…
Answer: How to convert .CEL file to .VCF file? by James W. MacDonald 57k
I don't know of anything within Bioconductor, but after a Google search for affy2vcf (hint), I came upon [this github repo][1]. [1]:…
Answer: DESeq2: One or more designs for contrasts of interest by Michael Love 33k
Sorry, I can only provide software support at this time. I don’t have time to provide statistical consultation on the support site. I’d rec…
Answer: DESeq2 - one groups with no replicates by Michael Love 33k
You can perform this analysis, it should run in DESeq2, but I believe there are also some specialized methods to give a single sample somet…
Answer: failing to install the package org.Hs.eg.db in R (version 4.0.5 ) by James W. MacDonald 57k
You need to supply more than just the error. But anyway, upgrade to R-4.1.0 and Bioconductor 3.13 and see if that fixes the problem.
Votes
Answer: DESeq2 - one groups with no replicates
Answer: DESeq2 - one groups with no replicates
pairwise combining factors or multifactor analysis ? (DESeq2)
Comment: Confusion using edgeR and spline-fitted data
Interpretation of confidence interval values for logFC returned from topTable function in limma with microarray dataset
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