Showing : SVA • reset
0
votes
3
replies
225
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 7 days ago by ▴ 850 • written 13 days ago by • 0
3
votes
6
replies
234
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
14 days ago nhaus ▴ 30
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
23 days ago • updated 22 days ago michelafrancesconi8 • 0
0
votes
4
replies
393
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
24 days ago • updated 23 days ago Lucy ▴ 60
0
votes
8
replies
379
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
7 weeks ago michelafrancesconi8 • 0
0
votes
3
replies
291
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 7 weeks ago by 65k • written 8 weeks ago by ▴ 10
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 ★ 4.0k • written 3 months ago by • 0
0
votes
1
reply
381
views
DESeq2 interaction term + sva
sva DESeq2
updated 3 months ago by 41k • written 4 months ago by ▴ 20
0
votes
2
replies
331
views
combat output NaN
sva
5 months ago maxixian1990 • 0
0
votes
4
replies
572
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 9 days ago by 41k • written 6 months ago by • 0
5
votes
2
replies
726
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 8 days ago by 50k • written 7 months ago by ▴ 10
0
votes
1
reply
444
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 8 months ago by 65k • written 8 months ago by ▴ 10
0
votes
2
replies
606
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 months ago by • 0
3
votes
3
replies
912
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
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 ★ 4.0k • written 10 months ago by ▴ 10
0
votes
0
replies
383
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
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: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Hi, Yes, I've tried this, but I am not sure if it is possible to assign `bquote` values to the names of a vector. In particular, if I use…
Votes
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?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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