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sva
•
reset
5
votes
2
replies
723
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
7 months ago
Federico
▴ 10
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 7 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
3
votes
6
replies
230
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
14 days ago • updated 13 days ago
nhaus
▴ 30
3
votes
3
replies
908
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
10 months ago • updated 9 months ago
amnahsiddiqa
▴ 10
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
James W. MacDonald
65k • written 8 months ago by
D-Bug
▴ 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 10 months ago by
ATpoint
★ 4.0k • written 10 months ago by
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
Hamza
• 0 • written 3.1 years ago by
zeegzaag
• 0
0
votes
5
replies
517
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 3 months ago by
ATpoint
★ 4.0k • written 3 months ago by
Xiao
• 0
0
votes
0
replies
380
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
10 months ago
amnahsiddiqa
▴ 10
0
votes
4
replies
566
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 8 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
1
reply
380
views
DESeq2 interaction term + sva
sva
DESeq2
updated 3 months ago by
Michael Love
41k • written 4 months ago by
marinaw
▴ 20
0
votes
8
replies
374
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
7 weeks ago • updated 6 weeks ago
michelafrancesconi8
• 0
0
votes
2
replies
329
views
combat output NaN
sva
5 months ago
maxixian1990
• 0
0
votes
1
reply
441
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl
sva
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
Shila
• 0
0
votes
4
replies
391
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
24 days ago • updated 22 days ago
Lucy
▴ 60
0
votes
2
replies
604
views
Fluidigm Data Batch Correction
sva
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Khushbu
• 0
0
votes
3
replies
289
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
MEME
▴ 10
0
votes
2
replies
153
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
23 days ago • updated 22 days ago
michelafrancesconi8
• 0
0
votes
3
replies
222
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 6 days ago by
W. Evan Johnson
▴ 850 • written 13 days ago by
schlumbohm
• 0
19 results • Page
1 of 1
Recent ...
Replies
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Votes
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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