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reset
1
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4
replies
1.9k
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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
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 8 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 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
2
votes
3
replies
1.1k
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
3
votes
3
replies
914
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
amnahsiddiqa
▴ 10
5
votes
2
replies
729
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
7 months ago
Federico
▴ 10
0
votes
2
replies
608
views
Fluidigm Data Batch Correction
sva
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Khushbu
• 0
0
votes
4
replies
573
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 9 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
5
replies
521
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
1
reply
446
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
395
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
25 days ago • updated 23 days ago
Lucy
▴ 60
0
votes
0
replies
385
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
1
reply
382
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
379
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
7 weeks ago
michelafrancesconi8
• 0
0
votes
2
replies
332
views
combat output NaN
sva
5 months ago
maxixian1990
• 0
0
votes
3
replies
292
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 7 weeks ago by
James W. MacDonald
65k • written 8 weeks ago by
MEME
▴ 10
3
votes
6
replies
236
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
15 days ago • updated 14 days ago
nhaus
▴ 30
0
votes
3
replies
227
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 7 days ago by
W. Evan Johnson
▴ 850 • written 14 days ago by
schlumbohm
• 0
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
24 days ago • updated 23 days ago
michelafrancesconi8
• 0
19 results • Page
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Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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