Showing : batch correction • reset
3
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fastMNN based correction for large multi-run experiment requires a similar population set in all the individual datasets?
scrna-seq integration batch correction
updated 5.7 years ago by ★ 29k • written 5.7 years ago by ▴ 40
0
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1
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Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 5.8 years ago by ★ 4.0k • written 5.8 years ago by • 0
5
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3
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batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2 batch correction
updated 5.8 years ago by 68k • written 5.8 years ago by ▴ 10
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3
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1.3k
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Diffbind batch effect blocking error
Diffbind ATAC batch correction blocking factor
updated 6.1 years ago by ★ 5.2k • written 6.1 years ago by • 0
1
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1
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1.3k
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All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2 differential expression batch correction design
updated 6.2 years ago by 43k • written 6.3 years ago by ▴ 40
4
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4
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2.0k
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 40
4
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5
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Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 6.5 years ago by ▴ 150 • written 6.5 years ago by ▴ 60
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Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by James W. MacDonald 68k
It may not be that common for bulk RNA-Seq, but in my experience it's very common for bulk miRNA-Seq.
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Nice. That's great to hear. `sva` was actually the next step I was planning to try. My colleagues haven't seen this kind of pattern before …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by James W. MacDonald 68k
It is not uncommon for library size to be apparent in an MDS plot. You can use `sva` or `RUV` to account for that.
Comment: p-adjusted values in multiple comparisons by Josh • 0
Yes, using lmFit with block and duplicateCorrelation is appropriate; mobile data collection can illustrate blocking importance. First estim…
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Understood, thanks. The issue I'm seeing is that even after normalization, the MDSplot still orders samples by library size. I suspect cell…
Votes
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: How to construct a BSgenome object from a custom genome assembly using BSgenomeF
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