Showing : batch-correction • reset
2
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4
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full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
2
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1
reply
1.3k
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batchelor batch correction correction runs into errors
batchelor batch-correction mnncorrect fastmnn rna-seq
updated 4.8 years ago by ★ 28k • written 5.5 years ago by ▴ 20
0
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8
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1.7k
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Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 10
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Answer: SingleR with multiple single cell references by Aaron Lun ★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies by ATpoint ★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Answer: To count or not to count multi-overlapping reads? by Gordon Smyth 52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2? by ATpoint ★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2? by Wolfgang Huber ★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
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A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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