Showing : sva • reset
1
vote
8
replies
2.1k
views
Error in running Combat function
sva ComBat
updated 4.6 years ago by ★ 4.0k • written 4.7 years ago by ▴ 10
0
votes
5
replies
1.7k
views
Variable of interest in combat correction
sva combat
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 10
0
votes
3
replies
1.5k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by • 0
0
votes
10
replies
1.8k
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
7
votes
6
replies
2.7k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 5.4 years ago by ▴ 870 • written 5.4 years ago by ▴ 10
0
votes
1
reply
1.1k
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 30
0
votes
1
reply
1.3k
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
1
vote
1
reply
1.3k
views
SVA paired samples
SVA EPIC methylation limma
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
2
votes
4
replies
1.5k
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
1
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2
replies
1.4k
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
0
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0
replies
2.8k
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
5.7 years ago anne.bozack • 0
0
votes
1
reply
1.3k
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 5.8 years ago by ▴ 870 • written 5.8 years ago by ▴ 10
0
votes
0
replies
1.1k
views
limma-voom group design and its effect on sva
limma voom group-design sva
5.8 years ago kentfung ▴ 20
0
votes
8
replies
2.0k
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 10
0
votes
3
replies
1.4k
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 5.9 years ago by 25k • written 5.9 years ago by • 0
2
votes
5
replies
2.1k
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 5.9 years ago by ★ 3.4k • written 6.0 years ago by • 0
0
votes
1
reply
1.4k
views
Handling adjustment variables and surrogate variables in model
sva deseq2
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
1
vote
1
reply
1.7k
views
Bioconductor SVA: two variables of interest
sva
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
4
votes
5
replies
1.3k
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 6.0 years ago by • 0 • written 6.0 years ago by ▴ 20
0
votes
2
replies
1.7k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
votes
3
replies
1.2k
views
Design matrix for cohort with samples outside "block"
limma voom sva
6.1 years ago kentfung ▴ 20
0
votes
0
replies
769
views
fsva function does not work without newdat argument
sva
6.1 years ago jakob.wirbel • 0
0
votes
0
replies
1.1k
views
The correct specification of the model matrix to ComBat
ComBat sva
6.1 years ago Sam ▴ 10
8
votes
4
replies
5.3k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 670
0
votes
0
replies
1.3k
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
6.2 years ago kentfung ▴ 20
1
vote
1
reply
2.0k
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq sva DSS
updated 6.2 years ago by ▴ 60 • written 6.3 years ago by ▴ 10
2
votes
8
replies
4.2k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
2
votes
1
reply
2.1k
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
6.3 years ago epibio ▴ 10
5
votes
3
replies
3.1k
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna coexpression sva
updated 6.3 years ago by ★ 3.0k • written 6.3 years ago by ▴ 280
0
votes
1
reply
1.1k
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 30
3
votes
12
replies
4.8k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 6.4 years ago by 68k • written 6.4 years ago by ▴ 10
1
vote
1
reply
1.3k
views
svaseq - over adjustment
svaseq sva
6.5 years ago flippy23 • 0
2
votes
17
replies
3.6k
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 2.9 years ago by 43k • written 6.5 years ago by • 0
1
vote
2
replies
2.0k
views
Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 6.6 years ago by ▴ 90 • written 6.6 years ago by ▴ 30
4
votes
4
replies
3.0k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 6.6 years ago by 53k • written 6.6 years ago by ▴ 680
0
votes
0
replies
1.5k
views
OpenBLAS issue with ComBat() function of the R SVA package on Torque cluster
sva R OpenBLAS
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
1
vote
1
reply
1.2k
views
sva correction for MEDIPS
MEDIPS svaseq sva
updated 6.6 years ago by ▴ 570 • written 6.6 years ago by • 0
1
vote
7
replies
1.9k
views
paired sample - SVA model matrix
limma sva paired sample
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
1
vote
1
reply
1.5k
views
Define batch effect variables before removing them or getting rid of hidden surrogate variables
batch effect correction sva proteomics
6.8 years ago Sebastian Hesse ▴ 70
1
vote
10
replies
8.1k
views
SVAseq and DESeq2 workflow
sva deseq2
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 10
0
votes
0
replies
717
views
Sva for tumor cellular heterogeneity
limma sva
6.9 years ago chp950 • 0
0
votes
2
replies
1.9k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
votes
0
replies
1.3k
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
7.0 years ago jmsendoya • 0
0
votes
1
reply
2.6k
views
A problem in using Combat
sva combat
updated 7.2 years ago by ▴ 870 • written 7.2 years ago by • 0
3
votes
4
replies
2.0k
views
Calling svaseq() multiple times
edger sva svaseq limma
updated 7.3 years ago by ★ 7.9k • written 7.3 years ago by ▴ 20
1
vote
6
replies
1.8k
views
differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
7.3 years ago aec ▴ 90
4
votes
8
replies
7.8k
views
Convert Normalized RNA-Seq counts to TPM after Batch Correction
sva deseq2 limma
updated 3.1 years ago by • 0 • written 7.4 years ago by ▴ 70
3
votes
7
replies
6.4k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 7.4 years ago by ▴ 30 • written 9.6 years ago by ▴ 40
8
votes
3
replies
5.9k
views
DESeq2 with interaction using SVA
deseq2 sva interaction term grouping variable deseq
7.6 years ago kevin.kingsland ▴ 70
1
vote
2
replies
4.1k
views
Applying SVA to RNA-Seq dataset
DESeq2 sva svaseq batch effect correction
7.6 years ago L_K • 0
240 results • Page 2 of 5
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Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Comment: Average biological replicates in RNA-seq by boczniak767 ▴ 740
@atpoint Should I first standardise data and then average replicates?
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Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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