Showing : sva • reset
0
votes
3
replies
218
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 5 days ago by ▴ 850 • written 11 days ago by • 0
3
votes
6
replies
226
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
12 days ago nhaus ▴ 30
0
votes
2
replies
149
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
21 days ago • updated 20 days ago michelafrancesconi8 • 0
0
votes
4
replies
390
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
22 days ago • updated 21 days ago Lucy ▴ 60
0
votes
8
replies
373
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 weeks ago michelafrancesconi8 • 0
0
votes
3
replies
288
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 7 weeks ago by 65k • written 7 weeks ago by ▴ 10
0
votes
5
replies
511
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
0
votes
1
reply
377
views
DESeq2 interaction term + sva
sva DESeq2
updated 3 months ago by 41k • written 4 months ago by ▴ 20
0
votes
2
replies
329
views
combat output NaN
sva
5 months ago maxixian1990 • 0
0
votes
4
replies
563
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 7 days ago by 41k • written 6 months ago by • 0
5
votes
2
replies
716
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
6 months ago Federico ▴ 10
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 6 days ago by 50k • written 7 months ago by ▴ 10
0
votes
1
reply
439
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
1.0k
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 8 months ago by 65k • written 8 months ago by ▴ 10
0
votes
2
replies
601
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 months ago by • 0
3
votes
3
replies
906
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
9 months ago amnahsiddiqa ▴ 10
2
votes
3
replies
1.1k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
0
votes
0
replies
379
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
9 months ago amnahsiddiqa ▴ 10
0
votes
1
reply
528
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
2
votes
2
replies
817
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
14 months ago Hatchet • 0
5
votes
2
replies
754
views
Sva and batch effect
limma BatchEffect sva
updated 14 months ago by 50k • written 14 months ago by • 0
0
votes
2
replies
777
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
20 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
672
views
Why does surrogate variable confound with variable given in mod?
sva
21 months ago shdam ▴ 10
1
vote
3
replies
1.3k
views
Error in shrinkage for DESeq2
sva DESeq2
22 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 6.5 years ago by ▴ 60
1
vote
1
reply
736
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
1
vote
2
replies
1.6k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
23 months ago takemoto • 0
0
votes
1
reply
908
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.0 years ago by 50k • written 2.0 years ago by • 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 ★ 4.0k • written 2.2 years ago by ▴ 30
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
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
3.5k
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
0
replies
779
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 2.9 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 2.9 years ago by ▴ 50 • written 2.9 years ago by • 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 3.1 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
971
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.2 years ago by ★ 4.0k • written 3.2 years ago by • 0
0
votes
0
replies
954
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.3 years ago epibio ▴ 10
1
vote
8
replies
1.4k
views
Error in running Combat function
sva ComBat
updated 3.2 years ago by ★ 3.9k • written 3.3 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
0
votes
3
replies
1.0k
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 3.6 years ago by 65k • written 3.6 years ago by • 0
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
0
votes
1
reply
756
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 30
0
votes
1
reply
961
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 4.1 years ago by 65k • written 4.1 years ago by • 0
1
vote
1
reply
937
views
SVA paired samples
SVA EPIC methylation limma
updated 4.1 years ago by 65k • written 4.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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