Showing : Batch Correction • reset
3
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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 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 40
0
votes
1
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1.4k
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Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by • 0
5
votes
3
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822
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batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2 batch correction
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 10
0
votes
3
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1.2k
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Diffbind batch effect blocking error
Diffbind ATAC batch correction blocking factor
updated 5.6 years ago by ★ 5.2k • written 5.6 years ago by • 0
1
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1
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1.2k
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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 5.7 years ago by 43k • written 5.7 years ago by ▴ 40
4
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4
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1.8k
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 40
4
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5
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2.2k
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Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 5.9 years ago by ▴ 150 • written 5.9 years ago by ▴ 60
7 results • Page 1 of 1
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Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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