Showing : SVA • reset
13
votes
11
replies
12k
views
RNA-Seq, generate batch-free count matrix
edgeR sva
updated 10.3 years ago by 52k • written 10.5 years ago by ▴ 90
4
votes
5
replies
11k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 5 months ago by • 0 • written 7.3 years ago by ▴ 60
10
votes
6
replies
11k
views
Estimating and removing batch effects from rna-seq dataset
sva batch effect rnaseq removebatcheffect() limma
updated 9.3 years ago by ▴ 650 • written 9.3 years ago by ▴ 110
5
votes
12
replies
8.2k
views
Remove batch effect in small RNASeq study (SVA or others?)
RNASeq Alignment edgeR sva
updated 10.0 years ago by 52k • written 10.8 years ago by ★ 1.0k
8
votes
3
replies
7.6k
views
Removing batch effects with sva and combat using the sva package
Regression limma sva Regression limma sva
updated 13.1 years ago by ▴ 60 • written 13.1 years ago by ▴ 650
1
vote
10
replies
7.5k
views
SVAseq and DESeq2 workflow
sva deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
1
vote
4
replies
7.4k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3.3 years ago NewBioInfo ▴ 10
2
votes
5
replies
6.9k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 20
4
votes
8
replies
6.9k
views
Convert Normalized RNA-Seq counts to TPM after Batch Correction
sva deseq2 limma
updated 2.4 years ago by • 0 • written 6.8 years ago by ▴ 70
0
votes
6
replies
6.9k
views
ComBat with multiple batches
sva combat 450k
9.0 years ago ben.run974 • 0
9
votes
8
replies
6.8k
views
sva + egdeR - differential expression analysis - RNA-seq data
sva edgeR
9.1 years ago mrodrigues.fernanda ▴ 10
2
votes
2
replies
6.6k
views
SVA: Error in svd((dats - rowMeans(dats))) : a dimension is zero
sva
updated 8.4 years ago by ▴ 650 • written 8.5 years ago by ▴ 30
3
votes
7
replies
6.1k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 6.8 years ago by ▴ 30 • written 9.0 years ago by ▴ 40
4
votes
3
replies
6.1k
views
svaseq: how many and which surrogate variables to pick
sva
updated 2.1 years ago by • 0 • written 9.4 years ago by ▴ 10
6
votes
6
replies
5.9k
views
Questions regarding SVA batch effect normalizazion into DeSeq2 workflow
sva deseq2 batch effect
updated 8.8 years ago by 43k • written 8.8 years ago by • 0
0
votes
2
replies
5.7k
views
sva + voom + limma
RNASeq Microarray sva RNASeq Microarray sva
updated 11.4 years ago by 52k • written 11.4 years ago by ▴ 120
8
votes
3
replies
5.4k
views
DESeq2 with interaction using SVA
deseq2 sva interaction term grouping variable deseq
7.0 years ago kevin.kingsland ▴ 70
12
votes
3
replies
5.4k
views
sva: how to incorporate adjusting variables
inveRsion sva inveRsion sva
updated 11.4 years ago by ▴ 650 • written 11.4 years ago by ▴ 120
3
votes
4
replies
5.2k
views
Running Combat in SVA with NA values in matrix
sva combat
9.1 years ago CC ▴ 10
0
votes
8
replies
5.2k
views
ComBat: 3 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
updated 10.9 years ago by ★ 13k • written 10.9 years ago by ★ 13k
4
votes
4
replies
4.9k
views
sva::ComBat without covariate of interest?
sva combat
updated 10.2 years ago by ▴ 870 • written 10.2 years ago by ▴ 110
0
votes
5
replies
4.8k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.0 years ago by ★ 4.6k • written 3.8 years ago by • 0
0
votes
1
reply
4.7k
views
Steps of removing batch effects and hidden variables
RNASeq Normalization sva RNASeq Normalization sva
updated 10.5 years ago by ▴ 330 • written 10.5 years ago by ★ 1.0k
10
votes
10
replies
4.6k
views
Method for batch correction
combat sva limma
updated 8.8 years ago by ▴ 120 • written 8.8 years ago by ▴ 60
8
votes
4
replies
4.6k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 5.5 years ago by 52k • written 5.5 years ago by ▴ 670
0
votes
1
reply
4.3k
views
SVA package error message: Error in diag(dims[2]) - mod %*% solve(t(mod) %*% mod) %*% t(mod) : non-conformable arrays
sva sva
11.5 years ago Ying Chen ▴ 110
0
votes
2
replies
4.3k
views
ComBat: Error when including numerical covariates in model (numCovs)
sva sva
updated 11.0 years ago by ▴ 20 • written 11.0 years ago by ▴ 870
0
votes
4
replies
4.3k
views
sva package
sva sva
updated 14.2 years ago by 21k • written 14.2 years ago by ▴ 90
5
votes
3
replies
4.3k
views
about SVA: matrix of corrected expression values
SVA COMBAT
8.3 years ago Bogdan ▴ 670
3
votes
12
replies
4.1k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 5.8 years ago by 67k • written 5.8 years ago by ▴ 10
1
vote
5
replies
4.1k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2 sva svaseq pca
8.6 years ago Peter Alto ▴ 10
0
votes
1
reply
4.0k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 3.7 years ago by • 0 • written 7.7 years ago by ▴ 10
4
votes
8
replies
3.9k
views
Visualising effects of observation/sample weights in differential expression analysis
limma voom sva edgeR
updated 9.9 years ago by ▴ 1000 • written 9.9 years ago by ▴ 20
1
vote
4
replies
3.9k
views
SVA package - for removing batch effect after DESeq - error in ComBat
sva combat
9.6 years ago GFM ▴ 20
4
votes
2
replies
3.9k
views
Difference between "be" and "leek" methods when deciding number of surrogate variables to estimate with SVA?
sva num.sv
7.6 years ago brhead ▴ 40
2
votes
8
replies
3.9k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 10
0
votes
2
replies
3.7k
views
Using sva ComBat on DESeq2 Data
deseq2 DE rnaseq sva combat
updated 9.0 years ago by 43k • written 9.0 years ago by • 0
1
vote
2
replies
3.7k
views
Applying SVA to RNA-Seq dataset
DESeq2 sva svaseq batch effect correction
7.0 years ago L_K • 0
7
votes
3
replies
3.5k
views
SVA: Including variable of interest in ComBat model matrix
combat sva SVA sva ComBat batch effect
updated 8.8 years ago by ▴ 870 • written 8.8 years ago by ▴ 20
2
votes
5
replies
3.4k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 7.3 years ago by ▴ 870 • written 7.3 years ago by • 0
5
votes
2
replies
3.4k
views
ComBat - Including variable of interest in model matrix?
combat sva
updated 10.2 years ago by ▴ 650 • written 10.2 years ago by ▴ 10
10
votes
4
replies
3.4k
views
Adjust for multiple batches using combat
combat sva limma
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
0
votes
2
replies
3.3k
views
Use surrogate variables on DESeq2
deseq2 sva deseq differential gene expression
updated 8.6 years ago by ▴ 20 • written 9.4 years ago by ▴ 40
4
votes
5
replies
3.3k
views
SVA and proportion of variance explained
sva svd explained variance pca
updated 8.3 years ago by ▴ 650 • written 8.3 years ago by ▴ 10
1
vote
2
replies
3.3k
views
Problem with n.sv in sva package
batch effect sva
9.5 years ago daih • 0
3
votes
4
replies
3.2k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
2
votes
17
replies
3.0k
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 2.2 years ago by 43k • written 5.8 years ago by • 0
0
votes
7
replies
2.9k
views
Applying sva is compatible with limma duplicateCorrelation?
limma-voom sva duplicatecorrelation
updated 7.5 years ago by ▴ 130 • written 7.5 years ago by ▴ 90
0
votes
1
reply
2.8k
views
Back-estimating batch variables from SVA for ComBat?
sva sva
updated 12.5 years ago by ▴ 260 • written 12.5 years ago by ▴ 120
0
votes
2
replies
2.8k
views
Remove batch effect - condition partially confounded by data
combat differential gene expression sva
updated 10.0 years ago by ▴ 650 • written 10.0 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…
Answer: Selection of correct coefficients or contrasts in DESeq2 by James W. MacDonald 67k
Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…
Comment: How to generate circular cnetplot and color nodes and edges in the same plot ? by Blandine • 0
Thank you so much ! It's working !
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by James W. MacDonald 67k
Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…
Comment: Recount3 data correspond to TCGA data by Leonardo Collado Torres ★ 1.1k
Thanks @fep29! ^^
Votes
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Awards • All
Popular Question to Robert Castelo ★ 3.4k
Popular Question to Robert Ivanek ▴ 750
Popular Question to shepherl 4.1k
Popular Question to Martin Morgan 25k
Popular Question to Guido Hooiveld ★ 4.1k
Locations • All
Canada, 1 minute ago
WEHI, Melbourne, Australia, 5 minutes ago
United States, 7 minutes ago
United States, 19 minutes ago
Pittsburgh, United States, 1 hour ago
Traffic: 528 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6