Showing : SVA • reset
2
votes
17
replies
2.3k
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 18 months ago by 41k • written 5.1 years ago by • 0
3
votes
12
replies
3.2k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 10
5
votes
12
replies
7.7k
views
Remove batch effect in small RNASeq study (SVA or others?)
RNASeq Alignment edgeR sva
updated 9.3 years ago by 50k • written 10.0 years ago by ★ 1.0k
13
votes
11
replies
12k
views
RNA-Seq, generate batch-free count matrix
edgeR sva
updated 9.5 years ago by 50k • written 9.8 years ago by ▴ 90
0
votes
10
replies
1.2k
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 3.6 years ago by 65k • written 3.6 years ago by • 0
1
vote
10
replies
6.2k
views
SVAseq and DESeq2 workflow
sva deseq2
updated 5.5 years ago by 41k • written 5.5 years ago by ▴ 10
10
votes
10
replies
4.0k
views
Method for batch correction
combat sva limma
updated 8.0 years ago by ▴ 110 • written 8.0 years ago by ▴ 60
2
votes
9
replies
1.6k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 21 months ago by 65k • written 21 months ago by • 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 8 days ago by 50k • written 7 months ago by ▴ 10
1
vote
8
replies
1.4k
views
Error in running Combat function
sva ComBat
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by ▴ 10
2
votes
8
replies
3.3k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 10
0
votes
8
replies
379
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
7 weeks ago michelafrancesconi8 • 0
4
votes
8
replies
3.2k
views
Visualising effects of observation/sample weights in differential expression analysis
limma voom sva edgeR
updated 9.2 years ago by ▴ 1000 • written 9.2 years ago by ▴ 20
4
votes
8
replies
5.7k
views
Convert Normalized RNA-Seq counts to TPM after Batch Correction
sva deseq2 limma
updated 20 months ago by • 0 • written 6.1 years ago by ▴ 70
0
votes
8
replies
1.4k
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 10
0
votes
8
replies
4.8k
views
ComBat: 3 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ★ 13k
9
votes
8
replies
6.1k
views
sva + egdeR - differential expression analysis - RNA-seq data
sva edgeR
8.3 years ago mrodrigues.fernanda ▴ 10
0
votes
7
replies
2.5k
views
Applying sva is compatible with limma duplicateCorrelation?
limma-voom sva duplicatecorrelation
updated 6.8 years ago by ▴ 130 • written 6.8 years ago by ▴ 90
0
votes
7
replies
1.7k
views
sva package for R 2.13.1?
sva sva
updated 12.7 years ago by 65k • written 12.7 years ago by ▴ 110
2
votes
7
replies
2.1k
views
ComBat Error: in solve.default(t(des) %*% des) : System is computationally singuar: ...
ComBat sva
8.9 years ago edammer • 0
3
votes
7
replies
5.4k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 6.1 years ago by ▴ 30 • written 8.2 years ago by ▴ 40
1
vote
7
replies
1.3k
views
paired sample - SVA model matrix
limma sva paired sample
updated 5.4 years ago by 65k • written 5.4 years ago by • 0
1
vote
6
replies
2.4k
views
normalization affects drastically limma-voom + sva results
normalization sva limma-voom
updated 6.8 years ago by 50k • written 6.8 years ago by ▴ 90
6
votes
6
replies
5.3k
views
Questions regarding SVA batch effect normalizazion into DeSeq2 workflow
sva deseq2 batch effect
updated 8.0 years ago by 41k • written 8.0 years ago by • 0
0
votes
6
replies
5.9k
views
ComBat with multiple batches
sva combat 450k
8.3 years ago ben.run974 • 0
3
votes
6
replies
238
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
15 days ago nhaus ▴ 30
1
vote
6
replies
2.4k
views
limma + voom + sva + complex RNA-seq design?
limma sva batch effect
7.4 years ago irenegallego • 0
1
vote
6
replies
1.3k
views
differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
6.0 years ago aec ▴ 90
7
votes
6
replies
1.6k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 4.0 years ago by ▴ 850 • written 4.0 years ago by ▴ 10
10
votes
6
replies
10k
views
Estimating and removing batch effects from rna-seq dataset
sva batch effect rnaseq removebatcheffect() limma
updated 8.5 years ago by ▴ 650 • written 8.5 years ago by ▴ 110
4
votes
5
replies
916
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 4.7 years ago by • 0 • written 4.7 years ago by ▴ 20
0
votes
5
replies
3.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.3 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
votes
5
replies
522
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
4
votes
5
replies
2.8k
views
SVA and proportion of variance explained
sva svd explained variance pca
updated 7.5 years ago by ▴ 650 • written 7.5 years ago by ▴ 10
0
votes
5
replies
1.0k
views
Variable of interest in combat correction
sva combat
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 10
1
vote
5
replies
1.7k
views
Paired design, normalisation and batch effects.
deseq2 eda sva rna-seq
updated 7.7 years ago by ▴ 610 • written 7.7 years ago by ▴ 10
2
votes
5
replies
2.8k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 6.6 years ago by ▴ 850 • written 6.6 years ago by • 0
0
votes
5
replies
1.2k
views
Clarification regarding analysis with multi-factorial design
limma multiple factor design sva voom
6.4 years ago scanchi • 0
1
vote
5
replies
3.7k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2 sva svaseq pca
7.9 years ago Peter Alto ▴ 10
2
votes
5
replies
1.4k
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 4.6 years ago by ★ 3.3k • written 4.6 years ago by • 0
2
votes
5
replies
5.8k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 20
0
votes
5
replies
2.0k
views
Problems installing sva and bladderbatch
sva sva
updated 12.5 years ago by 6.7k • written 12.5 years ago by ▴ 30
0
votes
5
replies
1.5k
views
use Combat to adjust for hidden variables without knowing batch effect
sva sva
10.8 years ago shirley zhang ★ 1.0k
0
votes
4
replies
1.6k
views
FeatureExpressionSet using list.files() in place of read.xysfiles()
Microarray Annotation GO Organism probe annotate limma convert pdInfoBuilder sva GO sva
updated 10.9 years ago by ★ 4.3k • written 10.9 years ago by ▴ 140
0
votes
4
replies
1.4k
views
Reproducibility of results with ComBat
sva combat
updated 8.7 years ago by ▴ 650 • written 8.7 years ago by • 0
7
votes
4
replies
3.9k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 4.8 years ago by 50k • written 4.8 years ago by ▴ 670
4
votes
4
replies
2.0k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 5.2 years ago by 50k • written 5.2 years ago by ▴ 660
1
vote
4
replies
3.5k
views
SVA package - for removing batch effect after DESeq - error in ComBat
sva combat
8.8 years ago GFM ▴ 20
0
votes
4
replies
3.7k
views
sva package
sva sva
updated 13.4 years ago by 21k • written 13.4 years ago by ▴ 90
3
votes
4
replies
1.7k
views
Taking surrogate variable into account before running PCA
sva svaseq
updated 6.9 years ago by ★ 3.9k • written 6.9 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 30
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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