Showing : SVA • reset
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
8
replies
373
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 weeks ago michelafrancesconi8 • 0
3
votes
6
replies
226
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
12 days ago nhaus ▴ 30
0
votes
5
replies
512
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
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
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
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
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
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
3
replies
219
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 5 days ago by ▴ 850 • written 11 days 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
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
5
votes
2
replies
717
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
6 months ago Federico ▴ 10
0
votes
2
replies
149
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
21 days ago michelafrancesconi8 • 0
0
votes
2
replies
329
views
combat output NaN
sva
5 months ago maxixian1990 • 0
0
votes
2
replies
603
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 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
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
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
19 results • Page 1 of 1
Recent ...
Replies
Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference by ATpoint ★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by Gayatri • 0
What I meant is even after deleting the NCBI.sqlite file, and re-running the script, an empty NCBI.sqlite file (0 kb) is created which is c…
Comment: DESeq2 output used for PCA plot on R studio by ATpoint ★ 4.0k
> Increase variability for mutants: use larger subtractive modifiers I was thinking the same as swbarnes. You're doing some data munging h…
Votes
Comment: get BM error
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
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