Showing : sva • reset
0
votes
2
replies
426
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 14 days ago by 52k • written 15 days ago by ▴ 10
0
votes
3
replies
408
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
12 weeks ago Travis • 0
4
votes
5
replies
11k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 4 months ago by • 0 • written 7.2 years ago by ▴ 60
0
votes
4
replies
912
views
Generating surrogate variables across multiple variables of interest
sva
5 months ago • updated 4 months ago Robert • 0
0
votes
3
replies
817
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 8 months ago by ▴ 870 • written 8 months ago by • 0
3
votes
6
replies
885
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
8 months ago nhaus ▴ 70
0
votes
2
replies
466
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
8 months ago michelafrancesconi8 • 0
0
votes
4
replies
883
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
8 months ago Lucy ▴ 60
0
votes
8
replies
873
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
9 months ago michelafrancesconi8 • 0
0
votes
3
replies
587
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 9 months ago by 67k • written 9 months ago by ▴ 10
0
votes
5
replies
1.3k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
0
votes
1
reply
702
views
DESeq2 interaction term + sva
sva DESeq2
updated 11 months ago by 43k • written 12 months ago by ▴ 20
0
votes
2
replies
604
views
combat output NaN
sva
13 months ago maxixian1990 • 0
0
votes
4
replies
982
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 8 months ago by 43k • written 14 months ago by • 0
5
votes
2
replies
1.8k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
15 months ago Federico ▴ 10
5
votes
9
replies
2.0k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 8 months ago by 52k • written 15 months ago by ▴ 10
0
votes
1
reply
770
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 16 months ago by 67k • written 16 months ago by • 0
2
votes
3
replies
2.0k
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 16 months ago by 67k • written 16 months ago by ▴ 10
0
votes
2
replies
889
views
Fluidigm Data Batch Correction
sva limma
updated 17 months ago by 52k • written 17 months ago by • 0
3
votes
3
replies
1.7k
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
18 months ago • updated 17 months ago amnahsiddiqa ▴ 10
2
votes
3
replies
1.9k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 18 months ago by ★ 4.6k • written 18 months ago by ▴ 10
0
votes
0
replies
584
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
18 months ago amnahsiddiqa ▴ 10
0
votes
1
reply
800
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 21 months ago by ★ 4.6k • written 21 months ago by • 0
2
votes
2
replies
1.1k
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
22 months ago Hatchet • 0
5
votes
2
replies
1.1k
views
Sva and batch effect
limma BatchEffect sva
updated 22 months ago by 52k • written 22 months ago by • 0
0
votes
2
replies
1.1k
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
2.4 years ago Marie • 0
2
votes
9
replies
2.0k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 2.4 years ago by 67k • written 2.4 years ago by • 0
1
vote
0
replies
833
views
Why does surrogate variable confound with variable given in mod?
sva
2.4 years ago shdam ▴ 10
1
vote
3
replies
1.7k
views
Error in shrinkage for DESeq2
sva DESeq2
2.5 years ago Kent • 0
1
vote
1
reply
929
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.6 years ago by 67k • written 2.6 years ago by ▴ 20
1
vote
2
replies
2.1k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
2.6 years ago takemoto • 0
0
votes
1
reply
1.3k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.7 years ago by 52k • written 2.7 years ago by • 0
1
vote
1
reply
1.5k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 2.8 years ago by ★ 4.6k • written 2.8 years ago by ▴ 70
1
vote
4
replies
2.0k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
2.8 years ago Clay • 0
0
votes
0
replies
1.3k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 2.9 years ago by 67k • written 2.9 years ago by • 0
0
votes
5
replies
4.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.9 years ago by ★ 4.6k • written 3.7 years ago by • 0
0
votes
0
replies
976
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
3.2 years ago georgia.katsoula ▴ 40
1
vote
4
replies
7.2k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3.3 years ago • updated 3.2 years ago NewBioInfo ▴ 10
1
vote
2
replies
1.7k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
3.4 years ago Ahdee ▴ 50
0
votes
1
reply
4.0k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 3.6 years ago by • 0 • written 7.7 years ago by ▴ 10
0
votes
1
reply
2.1k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 3.6 years ago by ▴ 50 • written 3.6 years ago by • 0
1
vote
4
replies
2.7k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 14 months ago by • 0 • written 3.8 years ago by • 0
0
votes
1
reply
1.7k
views
How to set mod0 in sva analysis
sva
updated 3.8 years ago by ★ 3.4k • written 3.8 years ago by • 0
2
votes
2
replies
1.3k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.8 years ago by ★ 4.6k • written 3.9 years ago by • 0
0
votes
0
replies
1.1k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.9 years ago epibio ▴ 10
1
vote
8
replies
1.8k
views
Error in running Combat function
sva ComBat
updated 3.9 years ago by ★ 4.0k • written 3.9 years ago by ▴ 10
0
votes
5
replies
1.3k
views
Variable of interest in combat correction
sva combat
updated 4.1 years ago by 67k • written 4.1 years ago by ▴ 10
0
votes
3
replies
1.3k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
0
votes
10
replies
1.5k
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 4.3 years ago by 67k • written 4.3 years ago by • 0
7
votes
6
replies
2.2k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 4.6 years ago by ▴ 870 • written 4.6 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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