Bioconductor Dds

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548

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DESeqDataSetFromMatrix dds DESeq2

updated 18 months ago by James W. MacDonald 68k • written 18 months ago by naomi.croft • 0

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695

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Celegans DESeq2 dds Errorinseq_len(length(idx)-1)

updated 2.4 years ago by James W. MacDonald 68k • written 2.4 years ago by Enzo.Scifo • 0

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1.4k

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deseq2 cooks distance dds

updated 6.6 years ago by Michael Love 43k • written 6.6 years ago by ipso • 0

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1.4k

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deseq2 dds RPKM

updated 6.9 years ago by Michael Love 43k • written 6.9 years ago by harry.horsnell.17 • 0

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2.5k

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deseq2 rld pheatmap dds

updated 7.4 years ago by Michael Love 43k • written 9.5 years ago by rahel14350 ▴ 10

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5.9k

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deseq2 DDS

updated 7.5 years ago by Michael Love 43k • written 7.5 years ago by rrcutler ▴ 70

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5.3k

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Deseq2 dds confounders

updated 9.3 years ago by Michael Love 43k • written 9.3 years ago by colaneri ▴ 30

7 results • Page 1 of 1

Recent ...

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Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k

We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…

Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k

It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…

Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20

I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…

Answer: Error in cnetplot by Guido Hooiveld ★ 4.1k

Unfortunately you did not show how you generated your input data (the object `enrichment`), nor did you show the output from `sessionInfo()…

Answer: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k

I think this is because Ensembl can assign different Gene IDs to "the same gene" if it is found both on a standard chromosome and a scaffol…

Votes

Answer: Explannation for ROAST results

Comment: Limma comparing gene expression between base line and one treatment

Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?

clusterProfiler-GO enrichment Error

A: Machine learning in R book

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