Bioconductor Batch-effect

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BatchQC RNA-seq R Shiny batch-effect

5.6 years ago manninm • 0

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edgeR batch-effect RNA-seq read counts ngs

updated 6.8 years ago by Aaron Lun ★ 29k • written 6.8 years ago by Roman ▴ 20

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batch-effect ruvseq

updated 8.0 years ago by James W. MacDonald 68k • written 8.0 years ago by llo ▴ 10

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rna-seq batch-effect combat scran sva

updated 8.1 years ago by Aaron Lun ★ 29k • written 8.1 years ago by firestar ▴ 20

4 results • Page 1 of 1

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Answer: Integration: Paired-end vs healthy single-end from a different source by wba64023 • 0

Interesting comparison! The source differences can definitely impact read quality and bias. Curious to see how you handle normalization bet…

Comment: Could we detect difference at pathway level but not significant different at gen by wba64023 • 0

thanks for sharing! [slope 2][1] [1]: https://slope2.online

Comment: After running samtools, the featureCounts command crashed. by eja.gssssse.r.m • 0

The buffer overflow detected error in your featureCount step usually indicates that the program is trying to write more data into memory …

Comment: gene Set with high AUC score but no cells assigned to cell type by eja.gssssse.r.m • 0

It sounds like your AUCell results may be showing high AUC scores without cell assignment due to thresholding or scoring cutoffs. Think of …

Answer: "Watched Tags" are being erased rather than updated by shepherl 4.2k

This should now be resolved

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Bioconductor 3.22 Released!

Comment: "Watched Tags" are being erased rather than updated

Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

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