Showing : SVA • reset
0
votes
4
replies
345
views
Generating surrogate variables across multiple variables of interest
sva
6 days ago • updated 6 hours ago Robert • 0
4
votes
4
replies
9.9k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 15 days ago by • 0 • written 6.8 years ago by ▴ 60
0
votes
3
replies
428
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 3 months ago by ▴ 850 • written 3 months ago by • 0
3
votes
6
replies
515
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
3 months ago nhaus ▴ 50
0
votes
2
replies
299
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
3 months ago michelafrancesconi8 • 0
0
votes
4
replies
568
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
3 months ago Lucy ▴ 60
0
votes
8
replies
604
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
4 months ago michelafrancesconi8 • 0
0
votes
3
replies
414
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 4 months ago by 66k • written 4 months ago by ▴ 10
0
votes
5
replies
811
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 6 months ago by ★ 4.2k • written 6 months ago by • 0
0
votes
1
reply
505
views
DESeq2 interaction term + sva
sva DESeq2
updated 6 months ago by 42k • written 7 months ago by ▴ 20
0
votes
2
replies
433
views
combat output NaN
sva
8 months ago maxixian1990 • 0
0
votes
4
replies
751
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 3 months ago by 42k • written 9 months ago by • 0
5
votes
2
replies
1.1k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
10 months ago Federico ▴ 10
5
votes
9
replies
1.6k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 3 months ago by 51k • written 10 months ago by ▴ 10
0
votes
1
reply
587
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 11 months ago by 66k • written 11 months ago by • 0
2
votes
3
replies
1.5k
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 11 months ago by 66k • written 11 months ago by ▴ 10
0
votes
2
replies
745
views
Fluidigm Data Batch Correction
sva limma
updated 12 months ago by 51k • written 12 months ago by • 0
3
votes
3
replies
1.2k
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
13 months ago amnahsiddiqa ▴ 10
2
votes
3
replies
1.5k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 13 months ago by ★ 4.2k • written 13 months ago by ▴ 10
0
votes
0
replies
458
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
13 months ago amnahsiddiqa ▴ 10
0
votes
1
reply
646
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 16 months ago by ★ 4.2k • written 16 months ago by • 0
2
votes
2
replies
954
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
17 months ago Hatchet • 0
5
votes
2
replies
876
views
Sva and batch effect
limma BatchEffect sva
updated 18 months ago by 51k • written 18 months ago by • 0
0
votes
2
replies
897
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
23 months ago Marie • 0
2
votes
9
replies
1.8k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 2.0 years ago by 66k • written 2.0 years ago by • 0
1
vote
0
replies
726
views
Why does surrogate variable confound with variable given in mod?
sva
2.0 years ago shdam ▴ 10
1
vote
3
replies
1.5k
views
Error in shrinkage for DESeq2
sva DESeq2
2.1 years ago Kent • 0
1
vote
1
reply
804
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.2 years ago by 66k • written 2.2 years ago by ▴ 20
1
vote
2
replies
1.8k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
2.2 years ago takemoto • 0
0
votes
1
reply
1.1k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.3 years ago by 51k • written 2.3 years ago by • 0
1
vote
1
reply
1.3k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 2.4 years ago by ★ 4.2k • written 2.4 years ago by ▴ 50
1
vote
4
replies
1.8k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
2.4 years ago Clay • 0
0
votes
0
replies
1.2k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 2.5 years ago by 66k • written 2.5 years ago by • 0
0
votes
5
replies
4.0k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.5 years ago by ★ 4.2k • written 3.3 years ago by • 0
0
votes
0
replies
849
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
2.8 years ago georgia.katsoula ▴ 40
1
vote
4
replies
6.3k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
2.8 years ago NewBioInfo ▴ 10
1
vote
2
replies
1.5k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
3.0 years ago Ahdee ▴ 50
0
votes
1
reply
3.6k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 3.2 years ago by • 0 • written 7.2 years ago by ▴ 10
0
votes
1
reply
1.8k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 3.2 years ago by ▴ 50 • written 3.2 years ago by • 0
1
vote
4
replies
2.2k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 9 months ago by • 0 • written 3.4 years ago by • 0
0
votes
1
reply
1.5k
views
How to set mod0 in sva analysis
sva
updated 3.4 years ago by ★ 3.3k • written 3.4 years ago by • 0
2
votes
2
replies
1.1k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.4 years ago by ★ 4.2k • written 3.4 years ago by • 0
0
votes
0
replies
1.0k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.5 years ago epibio ▴ 10
1
vote
8
replies
1.5k
views
Error in running Combat function
sva ComBat
updated 3.5 years ago by ★ 4.0k • written 3.5 years ago by ▴ 10
0
votes
5
replies
1.1k
views
Variable of interest in combat correction
sva combat
updated 3.7 years ago by 66k • written 3.7 years ago by ▴ 10
0
votes
3
replies
1.2k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
0
votes
10
replies
1.3k
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 3.9 years ago by 66k • written 3.9 years ago by • 0
7
votes
6
replies
1.8k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 4.2 years ago by ▴ 850 • written 4.2 years ago by ▴ 10
0
votes
1
reply
843
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 4.3 years ago by 66k • written 4.3 years ago by ▴ 30
0
votes
1
reply
1.0k
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 4.4 years ago by 66k • written 4.4 years ago by • 0
50 results • Page 1 of 1
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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Scholar to Michael Love 42k
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Scholar to Gordon Smyth 51k
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