Showing : SVA • reset
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
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
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
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
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
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
10
replies
1.7k
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
5
votes
9
replies
2.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 12 months ago by 52k • written 19 months ago by ▴ 10
2
votes
9
replies
2.3k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 2.7 years ago by 68k • written 2.8 years ago by • 0
2
votes
8
replies
4.1k
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
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
0
votes
8
replies
1.1k
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
13 months ago michelafrancesconi8 • 0
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
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
9
votes
8
replies
7.1k
views
sva + egdeR - differential expression analysis - RNA-seq data
sva edgeR
9.3 years ago mrodrigues.fernanda ▴ 10
1
vote
8
replies
2.0k
views
Error in running Combat function
sva ComBat
updated 4.2 years ago by ★ 4.0k • written 4.3 years ago by ▴ 10
0
votes
8
replies
1.9k
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 10
0
votes
7
replies
3.0k
views
Applying sva is compatible with limma duplicateCorrelation?
limma-voom sva duplicatecorrelation
updated 7.8 years ago by ▴ 130 • written 7.8 years ago by ▴ 90
0
votes
7
replies
2.1k
views
sva package for R 2.13.1?
sva sva
updated 13.7 years ago by 68k • written 13.7 years ago by ▴ 110
1
vote
7
replies
1.8k
views
paired sample - SVA model matrix
limma sva paired sample
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
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
2
votes
7
replies
2.6k
views
ComBat Error: in solve.default(t(des) %*% des) : System is computationally singuar: ...
ComBat sva
9.9 years ago edammer • 0
1
vote
6
replies
2.8k
views
normalization affects drastically limma-voom + sva results
normalization sva limma-voom
updated 7.8 years ago by 52k • written 7.8 years ago by ▴ 90
6
votes
6
replies
6.1k
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
1
vote
6
replies
1.6k
views
differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
6.9 years ago aec ▴ 90
7
votes
6
replies
2.5k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 5.0 years ago by ▴ 870 • written 5.0 years ago by ▴ 10
1
vote
6
replies
2.9k
views
limma + voom + sva + complex RNA-seq design?
limma sva batch effect
8.4 years ago irenegallego • 0
0
votes
6
replies
7.3k
views
ComBat with multiple batches
sva combat 450k
9.3 years ago ben.run974 • 0
3
votes
6
replies
1.2k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
12 months ago nhaus ▴ 70
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
3
votes
5
replies
1.1k
views
Overcoming confounding in batch effect correction
sva BiologicalQuestion
10 weeks ago • updated 9 weeks ago bbao ▴ 10
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
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
5
replies
1.5k
views
Variable of interest in combat correction
sva combat
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 10
0
votes
5
replies
1.6k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 15 months ago by ★ 4.8k • written 15 months ago by • 0
1
vote
5
replies
2.2k
views
Paired design, normalisation and batch effects.
deseq2 eda sva rna-seq
updated 8.7 years ago by ▴ 610 • written 8.7 years ago by ▴ 10
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
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
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
4
votes
5
replies
1.2k
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 5.7 years ago by • 0 • written 5.7 years ago by ▴ 20
2
votes
5
replies
1.9k
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 5.6 years ago by ★ 3.4k • written 5.6 years ago by • 0
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
5
replies
1.5k
views
Clarification regarding analysis with multi-factorial design
limma multiple factor design sva voom
7.4 years ago scanchi • 0
0
votes
5
replies
2.5k
views
Problems installing sva and bladderbatch
sva sva
updated 13.5 years ago by 6.7k • written 13.5 years ago by ▴ 30
0
votes
5
replies
1.9k
views
use Combat to adjust for hidden variables without knowing batch effect
sva sva
11.8 years ago shirley zhang ★ 1.0k
0
votes
4
replies
1.9k
views
FeatureExpressionSet using list.files() in place of read.xysfiles()
Microarray Annotation GO Organism probe annotate limma convert pdInfoBuilder sva GO sva
updated 11.9 years ago by ★ 4.3k • written 11.9 years ago by ▴ 140
0
votes
4
replies
1.8k
views
Reproducibility of results with ComBat
sva combat
updated 9.7 years ago by ▴ 650 • written 9.7 years ago by • 0
4
votes
4
replies
2.8k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 6.2 years ago by 52k • written 6.2 years ago by ▴ 680
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
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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