Showing : sva • reset
0
votes
3
replies
261
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 19 days ago by ▴ 850 • written 25 days ago by • 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 20 days ago by 50k • written 7 months ago by ▴ 10
0
votes
4
replies
603
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 21 days ago by 42k • written 6 months ago by • 0
3
votes
6
replies
280
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
26 days ago nhaus ▴ 30
0
votes
2
replies
174
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
5 weeks ago • updated 4 weeks ago michelafrancesconi8 • 0
0
votes
4
replies
433
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
5 weeks ago Lucy ▴ 60
0
votes
8
replies
412
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
8 weeks ago michelafrancesconi8 • 0
0
votes
3
replies
309
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 9 weeks ago by 65k • written 9 weeks ago by ▴ 10
0
votes
5
replies
569
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
1
reply
391
views
DESeq2 interaction term + sva
sva DESeq2
updated 4 months ago by 42k • written 4 months ago by ▴ 20
0
votes
2
replies
345
views
combat output NaN
sva
5 months ago maxixian1990 • 0
1
vote
4
replies
1.9k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 6 months ago by • 0 • written 3.2 years ago by • 0
5
votes
2
replies
763
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
7 months ago Federico ▴ 10
0
votes
1
reply
464
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 8 months ago by 65k • written 8 months ago by • 0
2
votes
3
replies
1.1k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 9 months ago by 65k • written 9 months ago by ▴ 10
0
votes
2
replies
625
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 months ago by • 0
3
votes
3
replies
937
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
10 months ago amnahsiddiqa ▴ 10
2
votes
3
replies
1.2k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
0
votes
0
replies
393
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
10 months ago amnahsiddiqa ▴ 10
0
votes
1
reply
543
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
2
votes
2
replies
843
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
15 months ago Hatchet • 0
5
votes
2
replies
774
views
Sva and batch effect
limma BatchEffect sva
updated 15 months ago by 50k • written 15 months ago by • 0
4
votes
3
replies
5.3k
views
svaseq: how many and which surrogate variables to pick
sva
updated 16 months ago by • 0 • written 8.7 years ago by ▴ 10
2
votes
17
replies
2.4k
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 18 months ago by 42k • written 5.1 years ago by • 0
4
votes
8
replies
5.8k
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
2
replies
801
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
21 months ago Marie • 0
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
1
vote
0
replies
679
views
Why does surrogate variable confound with variable given in mod?
sva
22 months ago shdam ▴ 10
1
vote
3
replies
1.4k
views
Error in shrinkage for DESeq2
sva DESeq2
23 months ago Kent • 0
4
votes
3
replies
9.2k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 23 months ago by • 0 • written 6.6 years ago by ▴ 60
1
vote
2
replies
1.6k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
23 months ago takemoto • 0
1
vote
1
reply
746
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 23 months ago by 65k • written 23 months ago by ▴ 20
0
votes
1
reply
939
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.1 years ago by 50k • written 2.1 years ago by • 0
4
votes
3
replies
2.0k
views
Blocked design and Surrogate Variables Analsysis(SVA)
limma sva block
updated 2.2 years ago by • 0 • written 9.5 years ago by ▴ 20
1
vote
4
replies
1.7k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
2.2 years ago Clay • 0
1
vote
1
reply
1.1k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 2.2 years ago by ★ 4.1k • written 2.2 years ago by ▴ 30
0
votes
0
replies
1.1k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 2.3 years ago by 65k • written 2.3 years ago by • 0
0
votes
5
replies
3.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.3 years ago by ★ 4.1k • written 3.1 years ago by • 0
0
votes
0
replies
790
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
2.6 years ago georgia.katsoula ▴ 40
1
vote
4
replies
5.8k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
2.6 years ago NewBioInfo ▴ 10
1
vote
2
replies
1.4k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
2.7 years ago Ahdee ▴ 50
0
votes
1
reply
3.4k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 3.0 years ago by • 0 • written 7.0 years ago by ▴ 10
0
votes
1
reply
1.6k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 3.0 years ago by ▴ 50 • written 3.0 years ago by • 0
0
votes
1
reply
1.3k
views
How to set mod0 in sva analysis
sva
updated 3.2 years ago by ★ 3.3k • written 3.2 years ago by • 0
2
votes
2
replies
987
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.2 years ago by ★ 4.1k • written 3.2 years ago by • 0
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
0
votes
0
replies
971
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.3 years ago epibio ▴ 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
0
votes
3
replies
1.1k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
0
votes
10
replies
1.2k
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 3.7 years ago by 65k • written 3.7 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cannot connect to ExperimentHub server by Jiayu • 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
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