Showing : SVA • reset
0
votes
3
replies
268
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A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 22 days ago by ▴ 850 • written 28 days ago by • 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 22 days ago by 50k • written 7 months ago by ▴ 10
0
votes
4
replies
610
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 24 days ago by 42k • written 6 months ago by • 0
3
votes
6
replies
285
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
29 days ago nhaus ▴ 30
0
votes
2
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176
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
5 weeks ago michelafrancesconi8 • 0
0
votes
4
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440
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
5 weeks ago Lucy ▴ 60
0
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8
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423
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
9 weeks ago michelafrancesconi8 • 0
0
votes
3
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314
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 9 weeks ago by 65k • written 10 weeks ago by ▴ 10
0
votes
5
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583
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
1
reply
394
views
DESeq2 interaction term + sva
sva DESeq2
updated 4 months ago by 42k • written 4 months ago by ▴ 20
0
votes
2
replies
345
views
combat output NaN
sva
5 months ago maxixian1990 • 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 3.2 years ago by • 0
5
votes
2
replies
769
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
1
reply
466
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 8 months ago by 65k • written 8 months ago by • 0
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 9 months ago by 65k • written 9 months ago by ▴ 10
0
votes
2
replies
631
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 10 months ago by • 0
3
votes
3
replies
947
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
2
votes
3
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1.2k
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 ★ 4.1k • written 10 months ago by ▴ 10
0
votes
0
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393
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How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
10 months ago amnahsiddiqa ▴ 10
19 results • Page 1 of 1
Recent ...
Replies
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE by maria.soler • 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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