Showing : SVA • reset
13
votes
11
replies
12k
views
RNA-Seq, generate batch-free count matrix
edgeR sva
updated 10.2 years ago by 52k • written 10.5 years ago by ▴ 90
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
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
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
10
votes
6
replies
11k
views
Estimating and removing batch effects from rna-seq dataset
sva batch effect rnaseq removebatcheffect() limma
updated 9.2 years ago by ▴ 650 • written 9.2 years ago by ▴ 110
9
votes
8
replies
6.8k
views
sva + egdeR - differential expression analysis - RNA-seq data
sva edgeR
9.1 years ago mrodrigues.fernanda ▴ 10
9
votes
2
replies
2.0k
views
Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
sva pca
updated 7.2 years ago by ▴ 120 • written 7.2 years ago by ★ 7.9k
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
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
8
votes
3
replies
7.5k
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
7
votes
3
replies
3.5k
views
SVA: Including variable of interest in ComBat model matrix
combat sva SVA sva ComBat batch effect
updated 8.7 years ago by ▴ 870 • written 8.7 years ago by ▴ 20
7
votes
6
replies
2.2k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 4.7 years ago by ▴ 870 • written 4.7 years ago by ▴ 10
6
votes
4
replies
1.7k
views
Combining newer/older RNAseq data, batch correcting
rnaseq limma sva batch effect voom
updated 8.2 years ago by ★ 28k • written 8.2 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
5
votes
3
replies
4.3k
views
about SVA: matrix of corrected expression values
SVA COMBAT
8.3 years ago Bogdan ▴ 670
5
votes
3
replies
2.2k
views
Problem using sva with limma for microarray DE analysis
sva limma
updated 8.3 years ago by ▴ 610 • written 8.3 years ago by ▴ 40
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 10.7 years ago by ★ 1.0k
5
votes
2
replies
1.8k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
15 months ago Federico ▴ 10
5
votes
1
reply
2.1k
views
Quantile normalization + sva for microarray experiment
sva quantile normalization microarray
updated 9.1 years ago by ★ 7.9k • written 9.1 years ago by ▴ 50
5
votes
2
replies
1.1k
views
Sva and batch effect
limma BatchEffect sva
updated 23 months ago by 52k • written 23 months ago by • 0
5
votes
9
replies
2.0k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 9 months ago by 52k • written 15 months ago by ▴ 10
5
votes
3
replies
2.7k
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna coexpression sva
updated 5.7 years ago by ★ 3.0k • written 5.7 years ago by ▴ 280
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
4
votes
4
replies
2.5k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 5.9 years ago by 52k • written 5.9 years ago by ▴ 660
4
votes
5
replies
3.2k
views
SVA and proportion of variance explained
sva svd explained variance pca
updated 8.2 years ago by ▴ 650 • written 8.2 years ago by ▴ 10
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
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
4
votes
2
replies
2.3k
views
PCA of bladderdata ("Batch effects and confounders" tutorial)
sva
updated 8.5 years ago by ▴ 180 • written 8.5 years ago by ▴ 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
4
votes
3
replies
6.0k
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
4
votes
5
replies
1.1k
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 5.4 years ago by • 0 • written 5.4 years ago by ▴ 20
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
4
votes
3
replies
2.3k
views
Blocked design and Surrogate Variables Analsysis(SVA)
limma sva block
updated 2.9 years ago by • 0 • written 10.2 years ago by ▴ 20
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
4
votes
0
replies
2.4k
views
sva: No significant surrogate variables
Microarray sva Microarray sva
11.8 years ago Shraddha Pai ▴ 80
3
votes
4
replies
1.8k
views
Calling svaseq() multiple times
edger sva svaseq limma
updated 6.7 years ago by ★ 7.9k • written 6.7 years ago by ▴ 20
3
votes
12
replies
4.0k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 5.7 years ago by 67k • written 5.7 years ago by ▴ 10
3
votes
1
reply
1.8k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 70
3
votes
4
replies
2.0k
views
Taking surrogate variable into account before running PCA
sva svaseq
updated 7.6 years ago by ★ 4.1k • written 7.6 years ago by • 0
3
votes
7
replies
6.0k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 6.8 years ago by ▴ 30 • written 8.9 years ago by ▴ 40
3
votes
6
replies
931
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
9 months ago nhaus ▴ 70
3
votes
4
replies
5.2k
views
Running Combat in SVA with NA values in matrix
sva combat
9.1 years ago CC ▴ 10
3
votes
3
replies
1.8k
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
18 months ago amnahsiddiqa ▴ 10
3
votes
3
replies
1.4k
views
Subsetting ELists and Applying sva to Iterative Differential Gene Expression Tests
limma edgeR sva RNA-Seq
updated 7.7 years ago by 52k • written 7.7 years ago by • 0
3
votes
2
replies
2.7k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma sva svaseq
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 670
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
2
votes
1
reply
2.0k
views
Regarding batch effect in Deseq2 package
deseq2 sva svaseq
updated 8.4 years ago by 43k • written 8.4 years ago by ▴ 20
2
votes
2
replies
6.5k
views
SVA: Error in svd((dats - rowMeans(dats))) : a dimension is zero
sva
updated 8.4 years ago by ▴ 650 • written 8.4 years ago by ▴ 30
2
votes
3
replies
1.7k
views
comBat/SVA with no "variable of interest" and two batches
combat sva covariates
updated 8.7 years ago by ▴ 420 • written 8.7 years ago by • 0
50 results • Page 1 of 1
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Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Michael Love 43k
hi, for questions about what statistical analysis approach to use, I recommend you work with a local statistician or someone familiar with …
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
I'm not certain that this will work with Oarfish, the documentation only mentions Salmon and piscem. I'd use tximport for now.
Answer: Problems with oarfish + tximport + swish by Michael Love 43k
> This is fine Did tximeta() print that a matching transcriptome was found?
Answer: DESeq2 Heatmap by swbarnes2 ★ 1.4k
> However, I've been asked why the first column (vehicle/control) isn't > entirely zero on the log fold change (logFC) expression scale. …
Comment: Biomart and ensembl not working? by James W. MacDonald 67k
``` > library(biomaRt) > mart <- useEnsembl("ensembl","hsapiens_gene_ensembl") Ensembl site unresponsive, trying useast mirror > mart Objec…
Votes
Answer: Limma Interaction Effect with Covariates
Comment: DESeq2 for single cell pseudobulk processing
C: Limma: how to get same output as topTable but for all the genes ?
A: Processing agilent data by limma
A: Linear regression in DESeq2
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