Showing : Batch Correction • reset
3
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3
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1.8k
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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 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 40
0
votes
1
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1.2k
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Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by • 0
5
votes
3
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777
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batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2 batch correction
updated 5.1 years ago by 67k • written 5.1 years ago by ▴ 10
0
votes
3
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1.1k
views
Diffbind batch effect blocking error
Diffbind ATAC batch correction blocking factor
updated 5.4 years ago by ★ 5.2k • written 5.4 years ago by • 0
1
vote
1
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1.1k
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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 5.5 years ago by 43k • written 5.5 years ago by ▴ 40
4
votes
4
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1.7k
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 40
4
votes
5
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2.1k
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Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 5.7 years ago by ▴ 150 • written 5.7 years ago by ▴ 60
7 results • Page 1 of 1
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Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
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