Showing : reference group • reset
9
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4
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3.3k
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Does edgeR need to specify reference group?
edgeR reference group
updated 6.2 years ago by 53k • written 6.2 years ago by ▴ 10
4
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4
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1.8k
views
edgeR: Choice of reference group in nested model
edgeR model.matrix nested design reference group
updated 7.6 years ago by ★ 29k • written 7.6 years ago by ▴ 40
5
votes
4
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5.3k
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limma, reference group, covariate
limma reference group covariate
11.0 years ago alakatos ▴ 130
3 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…
Votes
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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