Bioconductor Complex-design

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limma complex-design paired design

updated 7.7 years ago by Aaron Lun ★ 29k • written 7.7 years ago by ML18 ▴ 10

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rnaseqpower sspa sample size sequencing complex-design

updated 9.8 years ago by m.van_iterson ▴ 20 • written 9.8 years ago by roser.navarro • 0

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limma paired samples complex-design

10.0 years ago • updated 9.9 years ago aec ▴ 90

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4.8k

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limma model matrix limma design matrix complex-design

updated 10.5 years ago by Aaron Lun ★ 29k • written 10.5 years ago by Guido Hooiveld ★ 4.1k

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deseq2 multiple factor design complex-design

updated 10.7 years ago by Michael Love 43k • written 10.8 years ago by sifujio • 0

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combat software error rnaseq complex-design

updated 11.2 years ago by Peter Langfelder ★ 3.0k • written 11.2 years ago by Stefano Mangiola ▴ 40

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edgeR complex-design

updated 11.2 years ago by James W. MacDonald 68k • written 11.2 years ago by lwc628 ▴ 20

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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150

Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?

Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k

BTW, I tested with no issue on MacOS ARM on our previous github issue.

Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k

The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…

Answer: PTM analysis in LIMPA by Gordon Smyth 53k

For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…

Answer: problem reading bam files into nucleR by James W. MacDonald 68k

The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…

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C: DESeq2 Following RSEM

Upcoming Ensembl API and data access changes - new blog post available

Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?

Answer: Large logFC but somewhat high FDR

Comment: upstream git branches of bioc-release

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