Showing : SVA • reset
13
votes
11
replies
13k
views
RNA-Seq, generate batch-free count matrix
edgeR sva
updated 10.5 years ago by 52k • written 10.8 years ago by ▴ 90
4
votes
5
replies
12k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 8 months ago by • 0 • written 7.5 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 9.5 years ago by ▴ 650 • written 9.5 years ago by ▴ 110
5
votes
12
replies
8.4k
views
Remove batch effect in small RNASeq study (SVA or others?)
RNASeq Alignment edgeR sva
updated 10.3 years ago by 52k • written 11.0 years ago by ★ 1.0k
1
vote
4
replies
8.0k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3.6 years ago NewBioInfo ▴ 10
1
vote
10
replies
7.9k
views
SVAseq and DESeq2 workflow
sva deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
8
votes
3
replies
7.7k
views
Removing batch effects with sva and combat using the sva package
Regression limma sva Regression limma sva
updated 13.4 years ago by ▴ 60 • written 13.4 years ago by ▴ 650
4
votes
8
replies
7.4k
views
Convert Normalized RNA-Seq counts to TPM after Batch Correction
sva deseq2 limma
updated 2.7 years ago by • 0 • written 7.0 years ago by ▴ 70
2
votes
5
replies
7.4k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 20
0
votes
6
replies
7.3k
views
ComBat with multiple batches
sva combat 450k
9.3 years ago ben.run974 • 0
9
votes
8
replies
7.1k
views
sva + egdeR - differential expression analysis - RNA-seq data
sva edgeR
9.3 years ago mrodrigues.fernanda ▴ 10
2
votes
2
replies
6.8k
views
SVA: Error in svd((dats - rowMeans(dats))) : a dimension is zero
sva
updated 8.7 years ago by ▴ 650 • written 8.7 years ago by ▴ 30
4
votes
3
replies
6.3k
views
svaseq: how many and which surrogate variables to pick
sva
updated 2.4 years ago by • 0 • written 9.7 years ago by ▴ 10
3
votes
7
replies
6.3k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 7.1 years ago by ▴ 30 • written 9.2 years ago by ▴ 40
6
votes
6
replies
6.0k
views
Questions regarding SVA batch effect normalizazion into DeSeq2 workflow
sva deseq2 batch effect
updated 9.0 years ago by 43k • written 9.0 years ago by • 0
0
votes
2
replies
5.8k
views
sva + voom + limma
RNASeq Microarray sva RNASeq Microarray sva
updated 11.6 years ago by 52k • written 11.6 years ago by ▴ 120
8
votes
3
replies
5.7k
views
DESeq2 with interaction using SVA
deseq2 sva interaction term grouping variable deseq
7.2 years ago kevin.kingsland ▴ 70
3
votes
4
replies
5.6k
views
Running Combat in SVA with NA values in matrix
sva combat
9.4 years ago CC ▴ 10
12
votes
3
replies
5.5k
views
sva: how to incorporate adjusting variables
inveRsion sva inveRsion sva
updated 11.6 years ago by ▴ 650 • written 11.6 years ago by ▴ 120
0
votes
5
replies
5.3k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.3 years ago by ★ 4.8k • written 4.1 years ago by • 0
0
votes
8
replies
5.3k
views
ComBat: 3 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
updated 11.1 years ago by ★ 13k • written 11.1 years ago by ★ 13k
4
votes
4
replies
5.0k
views
sva::ComBat without covariate of interest?
sva combat
updated 10.4 years ago by ▴ 870 • written 10.4 years ago by ▴ 110
8
votes
4
replies
4.9k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 5.8 years ago by 52k • written 5.8 years ago by ▴ 670
10
votes
10
replies
4.9k
views
Method for batch correction
combat sva limma
updated 9.0 years ago by ▴ 120 • written 9.0 years ago by ▴ 60
0
votes
1
reply
4.8k
views
Steps of removing batch effects and hidden variables
RNASeq Normalization sva RNASeq Normalization sva
updated 10.7 years ago by ▴ 330 • written 10.7 years ago by ★ 1.0k
0
votes
4
replies
4.5k
views
sva package
sva sva
updated 14.4 years ago by 21k • written 14.4 years ago by ▴ 90
3
votes
12
replies
4.5k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 10
0
votes
1
reply
4.5k
views
SVA package error message: Error in diag(dims[2]) - mod %*% solve(t(mod) %*% mod) %*% t(mod) : non-conformable arrays
sva sva
11.7 years ago Ying Chen ▴ 110
0
votes
2
replies
4.5k
views
ComBat: Error when including numerical covariates in model (numCovs)
sva sva
updated 11.3 years ago by ▴ 20 • written 11.3 years ago by ▴ 870
5
votes
3
replies
4.4k
views
about SVA: matrix of corrected expression values
SVA COMBAT
8.6 years ago Bogdan ▴ 670
4
votes
8
replies
4.2k
views
Visualising effects of observation/sample weights in differential expression analysis
limma voom sva edgeR
updated 10.1 years ago by ▴ 1000 • written 10.2 years ago by ▴ 20
1
vote
5
replies
4.2k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2 sva svaseq pca
8.9 years ago Peter Alto ▴ 20
0
votes
1
reply
4.1k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 3.9 years ago by • 0 • written 8.0 years ago by ▴ 10
2
votes
8
replies
4.0k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
4
votes
2
replies
4.0k
views
Difference between "be" and "leek" methods when deciding number of surrogate variables to estimate with SVA?
sva num.sv
7.8 years ago brhead ▴ 40
1
vote
4
replies
4.0k
views
SVA package - for removing batch effect after DESeq - error in ComBat
sva combat
9.8 years ago GFM ▴ 20
1
vote
2
replies
3.9k
views
Applying SVA to RNA-Seq dataset
DESeq2 sva svaseq batch effect correction
7.2 years ago L_K • 0
0
votes
2
replies
3.8k
views
Using sva ComBat on DESeq2 Data
deseq2 DE rnaseq sva combat
updated 9.2 years ago by 43k • written 9.2 years ago by • 0
10
votes
4
replies
3.6k
views
Adjust for multiple batches using combat
combat sva limma
updated 8.1 years ago by ★ 28k • written 8.1 years ago by • 0
2
votes
5
replies
3.6k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 7.6 years ago by ▴ 870 • written 7.6 years ago by • 0
7
votes
3
replies
3.6k
views
SVA: Including variable of interest in ComBat model matrix
combat sva SVA sva ComBat batch effect
updated 9.0 years ago by ▴ 870 • written 9.0 years ago by ▴ 20
5
votes
2
replies
3.5k
views
ComBat - Including variable of interest in model matrix?
combat sva
updated 10.4 years ago by ▴ 650 • written 10.4 years ago by ▴ 10
3
votes
4
replies
3.4k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
4
votes
5
replies
3.4k
views
SVA and proportion of variance explained
sva svd explained variance pca
updated 8.5 years ago by ▴ 650 • written 8.5 years ago by ▴ 10
0
votes
2
replies
3.4k
views
Use surrogate variables on DESeq2
deseq2 sva deseq differential gene expression
updated 8.9 years ago by ▴ 20 • written 9.7 years ago by ▴ 40
1
vote
2
replies
3.3k
views
Problem with n.sv in sva package
batch effect sva
9.7 years ago daih • 0
2
votes
17
replies
3.3k
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 2.5 years ago by 43k • written 6.1 years ago by • 0
1
vote
4
replies
3.2k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 18 months ago by • 0 • written 4.1 years ago by • 0
0
votes
7
replies
3.0k
views
Applying sva is compatible with limma duplicateCorrelation?
limma-voom sva duplicatecorrelation
updated 7.7 years ago by ▴ 130 • written 7.7 years ago by ▴ 90
0
votes
3
replies
2.9k
views
can we use sva function to estimate artifacts for rna seq data?
sva svaseq batcheffectcorrection
updated 8.7 years ago by ▴ 650 • written 8.7 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much for the vis suggestion!
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much - I appreciate the mathematical explanation and link to Dr. Phipson's thesis!
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much - this is very clear!
Answer: How do I set up my DESeq analysis when I know a few vehicle control samples prov by Michael Love 43k
I think it will capture it automatically. E.g. if you use the method that focuses on genes lowly or not affected by the treatment, then the…
Votes
Comment: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
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