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 8 weeks ago by • 0 • written 4.2 years ago by ▴ 10
0
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1
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145
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 9 weeks ago by ▴ 50 • written 9 weeks ago by • 0
0
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2
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234
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How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
4 months ago Xiaojie Cheng • 0
0
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3
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220
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ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 4 months ago by 3.2k • written 4 months ago by • 0
0
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1
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127
views
How to set mod0 in sva analysis
sva
updated 5 months ago by ★ 2.7k • written 5 months ago by • 0
2
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2
replies
181
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 5 months ago by ▴ 700 • written 5 months ago by • 0
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0
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235
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
6 months ago Papyrus ▴ 10
1
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8
replies
338
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Error in running Combat function
sva ComBat
updated 6 months ago by 3.2k • written 6 months ago by ▴ 10
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5
replies
186
views
Variable of interest in combat correction
sva combat
updated 8 months ago by 57k • written 8 months ago by ▴ 10
0
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3
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215
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Extracting a subset of samples following SVA
Combat SVA Limma
updated 9 months ago by 3.2k • written 10 months ago by • 0
0
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10
replies
239
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 10 months ago by 57k • written 10 months ago by • 0
7
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6
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258
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sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 14 months ago by ▴ 840 • written 14 months ago by ▴ 10
0
votes
1
reply
127
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 15 months ago by 57k • written 15 months ago by ▴ 20
0
votes
1
reply
134
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 16 months ago by 57k • written 16 months ago by • 0
1
vote
1
reply
139
views
SVA paired samples
SVA EPIC methylation limma
updated 16 months ago by 57k • written 16 months ago by • 0
2
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4
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199
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 17 months ago by 33k • written 17 months ago by • 0
1
vote
2
replies
178
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 18 months ago by 43k • written 18 months ago by • 0
0
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0
replies
429
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
18 months ago anne.bozack • 0
0
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1
reply
216
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 19 months ago by ▴ 840 • written 19 months ago by ▴ 10
0
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0
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178
views
limma-voom group design and its effect on sva
limma voom group-design sva
19 months ago kentfung • 0
0
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8
replies
275
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 20 months ago by 57k • written 20 months ago by ▴ 10
0
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3
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248
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 21 months ago by 25k • written 21 months ago by • 0
2
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5
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379
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 22 months ago by ★ 2.7k • written 22 months ago by • 0
0
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1
reply
266
views
Handling adjustment variables and surrogate variables in model
sva deseq2
updated 22 months ago by 57k • written 22 months ago by • 0
1
vote
1
reply
261
views
Bioconductor SVA: two variables of interest
sva
updated 22 months ago by 57k • written 22 months ago by • 0
4
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5
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299
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 23 months ago by • 0 • written 23 months ago by • 0
0
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2
replies
228
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 23 months ago by 33k • written 23 months ago by • 0
0
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3
replies
235
views
Design matrix for cohort with samples outside "block"
limma voom sva
23 months ago kentfung • 0
0
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0
replies
171
views
fsva function does not work without newdat argument
sva
23 months ago jakob.wirbel • 0
0
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0
replies
255
views
The correct specification of the model matrix to ComBat
ComBat sva
23 months ago Sam ▴ 10
7
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4
replies
1.5k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 2.0 years ago by 43k • written 2.0 years ago by ▴ 620
0
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0
replies
291
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
2.0 years ago kentfung • 0
0
votes
1
reply
326
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq sva DSS
updated 2.1 years ago by ▴ 60 • written 2.1 years ago by • 0
1
vote
8
replies
770
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 2.1 years ago by 33k • written 2.1 years ago by • 0
2
votes
1
reply
445
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
2.2 years ago Papyrus ▴ 10
5
votes
3
replies
585
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna coexpression sva
updated 2.2 years ago by ★ 2.6k • written 2.2 years ago by ▴ 230
0
votes
1
reply
264
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 2.2 years ago by 33k • written 2.2 years ago by ▴ 20
3
votes
12
replies
1.0k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 2.2 years ago by 57k • written 2.2 years ago by ▴ 10
1
vote
1
reply
306
views
svaseq - over adjustment
svaseq sva
2.3 years ago flippy23 • 0
0
votes
8
replies
436
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 2.3 years ago by 33k • written 2.3 years ago by • 0
1
vote
2
replies
490
views
Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 2.4 years ago by ▴ 80 • written 2.4 years ago by ▴ 20
4
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4
replies
647
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 570
0
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0
replies
476
views
OpenBLAS issue with ComBat() function of the R SVA package on Torque cluster
sva R OpenBLAS
updated 2.4 years ago by 57k • written 2.4 years ago by • 0
4
votes
2
replies
4.0k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 2.5 years ago by • 0 • written 3.8 years ago by ▴ 60
1
vote
1
reply
356
views
sva correction for MEDIPS
MEDIPS svaseq sva
updated 2.5 years ago by ▴ 550 • written 2.5 years ago by • 0
0
votes
7
replies
544
views
paired sample - SVA model matrix
limma sva paired sample
updated 2.6 years ago by 57k • written 2.6 years ago by • 0
1
vote
1
reply
517
views
Define batch effect variables before removing them or getting rid of hidden surrogate variables
batch effect correction sva proteomics
2.7 years ago Sebastian Hesse ▴ 50
1
vote
10
replies
2.1k
views
SVAseq and DESeq2 workflow
sva deseq2
updated 2.8 years ago by 33k • written 2.8 years ago by • 0
0
votes
0
replies
293
views
Sva for tumor cellular heterogeneity
limma sva
2.8 years ago chp950 • 0
0
votes
2
replies
604
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 2.8 years ago by 33k • written 2.8 years ago by • 0
50 results • Page 1 of 1
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Comment: edgeR by Gitanjali • 0
Thanks @gordonsmyth , that helped. Also how do I put 24h at the end? I want to plot the observed and fitted values for each gene across tim…
Comment: ChIPseeker genomicAnnotationPriority by hqlkjx • 0
I am meeting the same problem
Comment: cannot install edgeR on M1 Mac by Gordon Smyth 43k
OK, I understand now the issue is that you are running R compiled for the Mac M1 ARM-based processor but Bioconductor doesn't provide binar…
Comment: How can I use geom_label_repel with EnhancedVolcano? by Kevin Blighe 3.2k
Thanks! I think that I know what you want to do, but, unfortunately, that level of customisation is not possible with *EnhancedVolcano* alo…
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Thank you, I've edited the post with the correct package, mzID.
Votes
ChIPseeker genomicAnnotationPriority
Answer: barcodeRanks unusual warning "In smooth.spline(x[new.keep], y[new.keep], df = df
Answer: barcodeRanks unusual warning "In smooth.spline(x[new.keep], y[new.keep], df = df
cannot install edgeR on M1 Mac
Increasing rlm iterations for convergence in limma's normalizeRobustSpline
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