Bioconductor ResultsNames

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DESeq2 resultsNames lfcShrink

updated 3.3 years ago by ATpoint ★ 5.0k • written 3.3 years ago by eve.olszanowski • 0

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resultsNames DESeq2 coefficient

4.6 years ago Jane ▴ 10

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resultsNames DESeq2

written 4.9 years ago by efratsh ▴ 10

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pairwise deseq2 extracting contrasts resultsnames results deseq2

updated 7.0 years ago by Michael Love 43k • written 7.0 years ago by Ricardo Rodrigues • 0

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deseq2 resultsnames batch effect contrast

updated 8.2 years ago by Michael Love 43k • written 8.2 years ago by pkachroo ▴ 10

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deseq2 DESeq2 resultsNames

8.4 years ago davichen ▴ 10

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deseq2 resultsnames

updated 8.4 years ago by Michael Love 43k • written 8.4 years ago by mrigaya.mehra ▴ 10

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deseq2 rnaseq resultsnames

8.6 years ago zeynep.nenseth • 0

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DESeq deseq2 resultsnames

9.5 years ago • updated 9.4 years ago akaever ▴ 30

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deseq2 resultsnames multifactorial design

updated 9.5 years ago by Michael Love 43k • written 9.5 years ago by Ira ▴ 10

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deseq2 relevel resultsNames multifactorial design

updated 9.8 years ago by Michael Love 43k • written 9.8 years ago by rclaire ▴ 20

11 results • Page 1 of 1

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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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Popular Question to James W. MacDonald 68k