Showing : sva • reset
0
votes
3
replies
201
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 1 day ago by ▴ 850 • written 8 days ago by • 0
3
votes
6
replies
217
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
9 days ago • updated 8 days ago nhaus ▴ 30
0
votes
2
replies
145
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
18 days ago • updated 17 days ago michelafrancesconi8 • 0
0
votes
4
replies
387
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
19 days ago • updated 17 days ago Lucy ▴ 60
0
votes
8
replies
370
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 weeks ago michelafrancesconi8 • 0
0
votes
3
replies
278
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 6 weeks ago by 65k • written 7 weeks ago by ▴ 10
0
votes
5
replies
498
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
370
views
DESeq2 interaction term + sva
sva DESeq2
updated 3 months ago by 41k • written 4 months ago by ▴ 20
0
votes
2
replies
325
views
combat output NaN
sva
5 months ago maxixian1990 • 0
0
votes
4
replies
558
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 3 days ago by 41k • written 5 months ago by • 0
5
votes
2
replies
699
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 2 days ago by 50k • written 6 months ago by ▴ 10
0
votes
1
reply
432
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 7 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
598
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 months ago by • 0
3
votes
3
replies
895
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
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
19 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
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