Showing : sva • reset
0
votes
3
replies
227
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 8 days ago by ▴ 850 • written 14 days ago by • 0
3
votes
6
replies
238
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
15 days ago nhaus ▴ 30
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
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 24 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
292
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
522
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
382
views
DESeq2 interaction term + sva
sva DESeq2
updated 3 months ago by 41k • written 4 months ago by ▴ 20
0
votes
2
replies
332
views
combat output NaN
sva
5 months ago maxixian1990 • 0
0
votes
4
replies
573
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 10 days ago by 41k • written 6 months ago by • 0
5
votes
2
replies
731
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
447
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
608
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 months ago by • 0
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
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
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
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
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
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…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
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
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