Showing : sva • reset
0
votes
2
replies
596
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 months ago by • 0
5
votes
2
replies
696
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
4
replies
386
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
18 days ago • updated 17 days ago Lucy ▴ 60
0
votes
3
replies
276
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 6 weeks ago by 65k • written 7 weeks ago by ▴ 10
0
votes
2
replies
143
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
17 days ago • updated 16 days ago michelafrancesconi8 • 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
368
views
DESeq2 interaction term + sva
sva DESeq2
updated 3 months ago by 41k • written 4 months ago by ▴ 20
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
5
replies
497
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
3
votes
3
replies
893
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
0
votes
4
replies
556
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
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
8
replies
366
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 weeks ago michelafrancesconi8 • 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
1
reply
431
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 7 months ago by 65k • written 7 months ago by • 0
0
votes
2
replies
324
views
combat output NaN
sva
5 months ago maxixian1990 • 0
0
votes
3
replies
196
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 1 day ago by ▴ 850 • written 7 days ago by • 0
0
votes
0
replies
378
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
3
votes
6
replies
211
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
8 days ago nhaus ▴ 30
19 results • Page 1 of 1
Recent ...
Replies
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…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Votes
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
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Awards • All
Popular Question to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Popular Question to BioinfGuru ▴ 30
Popular Question to Gordon Smyth 50k
Scholar to Peter Hickey ▴ 740
Locations • All
United States, 6 minutes ago
Vietnam, 9 minutes ago
WEHI, Melbourne, Australia, 16 minutes ago
France, 19 minutes ago
United States, 23 minutes ago
Traffic: 553 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6