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5
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9
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2.2k
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Batch correction and repeated measures
RUVSeq sva limma
updated 11 months ago by 52k • written 18 months ago by ▴ 10
4
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5
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12k
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[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 7 months ago by • 0 • written 7.4 years ago by ▴ 60
3
votes
6
replies
1.1k
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
11 months ago nhaus ▴ 70
3
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5
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1.1k
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Overcoming confounding in batch effect correction
sva BiologicalQuestion
5 weeks ago • updated 4 weeks ago bbao ▴ 10
0
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4
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1.1k
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 11 months ago by 43k • written 17 months ago by • 0
0
votes
3
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1.2k
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A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 11 months ago by ▴ 870 • written 11 months ago by • 0
0
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4
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1.1k
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
11 months ago Lucy ▴ 60
0
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2
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549
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
11 months ago michelafrancesconi8 • 0
0
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2
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569
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 3 months ago by 52k • written 3 months ago by ▴ 10
0
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3
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649
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
5 months ago Travis • 0
0
votes
4
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1.1k
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Generating surrogate variables across multiple variables of interest
sva
8 months ago • updated 7 months ago Robert • 0
11 results • Page 1 of 1
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Comment: DESEQ2 looking at main effects while controlling for a continuous variable by James W. MacDonald 68k
The covariate is accounted for when you fit the model, so you don't need to do anything with it at the contrast step. You don't need a con…
Comment: DESEQ2 looking at main effects while controlling for a continuous variable by Lennie • 0
Thank you so much for taking the time and for the detailed explanation! I was wondering, in your numeric contrast of c(1, -1, 0,0,0), doe…
Answer: DESEQ2 looking at main effects while controlling for a continuous variable by James W. MacDonald 68k
If you use a factor effects model (with an intercept), then you will have a baseline group (the intercept), and all other coefficients exce…
Comment: Issue with DECIPHER::IdTaxa by Daniel • 0
The issue is still there and it is a real pain. ape and ade4 are used by packages like Phyloseq. There should be a way to avoid these inc…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Gordon Smyth 52k
I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…
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Answer: DESEQ2 looking at main effects while controlling for a continuous variable
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
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